Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	ACB143	5,593,070	T→C	12.9%	Y66C (TAT→TGT)	thiC ←	Phosphomethylpyrimidine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	5,593,070	0	T	C	12.9%	147.1 / 13.0	54	Y66C (TAT→TGT)	thiC	Phosphomethylpyrimidine synthase
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base C (3/4);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACCGAAGTCGGAGCTCAGGCCTTCCAGGCGCTCGGTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTGCA  >  ACB143/5592936‑5593205                                                                                                                                       |                                                                                                                                        gACCGAAGTCGGAGCTCAGGCCTTCCAGGCGCTCGGTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATa                                                                                                                                        >  3:135186/1‑136 (MQ=255)       aGTCGGAGCTCAGGCCTTCCAGGCGCTCGGTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAg                                                                                                                                  >  5:245955/1‑136 (MQ=255)         tCGGAGCTCAGGCCTTCCAGGCGCTCGGTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCACACACCAGCa                                                                                                                                <  2:161177/136‑1 (MQ=255)          cGGAGCTCAGGCCTTCCAGGCGCTCGGTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCACGCACCAGCAc                                                                                                                               >  8:129059/1‑136 (MQ=255)                                   ggTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGaaa                                                                                                      >  1:241406/1‑136 (MQ=255)                                    gtgtCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAAt                                                                                                     <  7:77172/136‑1 (MQ=255)                                     tgtCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAAtc                                                                                                    <  6:82026/136‑1 (MQ=255)                                            gcgGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCggg                                                                                             <  6:283189/136‑1 (MQ=255)                                                gCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTGTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCACACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGgtct                                                                                         >  2:99281/1‑134 (MQ=255)                                                 cTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTc                                                                                        <  3:62442/136‑1 (MQ=255)                                                 cTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTc                                                                                        <  3:235045/136‑1 (MQ=255)                                                  ttCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGCCGTGTCATGCACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCa                                                                                       >  3:189151/1‑136 (MQ=255)                                                  ttCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCa                                                                                       >  6:275647/1‑136 (MQ=255)                                                  ttCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCa                                                                                       >  2:7540/1‑136 (MQ=255)                                                  ttCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCa                                                                                       >  4:126075/1‑136 (MQ=255)                                                  ttCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCa                                                                                       >  5:39590/1‑136 (MQ=255)                                                     gATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCACACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATcc                                                                                    <  5:56278/136‑1 (MQ=255)                                                                aaCGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTc                                                                         <  3:181490/136‑1 (MQ=255)                                                                aaCGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTc                                                                         <  4:185029/136‑1 (MQ=255)                                                                   gCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAAtcg                                                                                                   <  3:9199/107‑1 (MQ=255)                                                                   gCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAAtcg                                                                                                   >  4:9199/1‑107 (MQ=255)                                                                   gCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACg                                                                      <  7:120978/136‑1 (MQ=255)                                                                   gCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACg                                                                      <  6:39590/136‑1 (MQ=255)                                                                   gCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACg                                                                      >  8:190303/1‑136 (MQ=255)                                                                                 ccTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGa                                                        >  4:81508/1‑136 (MQ=255)                                                                                   tttGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATg                                                      >  4:50313/1‑136 (MQ=255)                                                                                        gcACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCgg                                                 >  1:72423/1‑136 (MQ=255)                                                                                         cACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCggg                                                <  8:211405/136‑1 (MQ=255)                                                                                             tCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGAGTTTGAATATCCGCAGAAATAGGTAGGGGTGTCATCCAGGCTGATTTCACGAATGGGTCAAAGGATGTCCGGGagcg                                            >  4:206502/1‑136 (MQ=255)                                                                                               gatgatCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAg                                          <  6:138092/136‑1 (MQ=255)                                                                                               gatgatCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAg                                          <  1:20775/136‑1 (MQ=255)                                                                                               gatgatCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAg                                          <  7:55991/136‑1 (MQ=255)                                                                                               gatgatCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAg                                          <  5:199479/136‑1 (MQ=255)                                                                                               gatgatCACGGCGGGGGAGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGTTTTCACGCATGGGGACACGGATGTCCGGGCGCGAg                                          <  2:289072/136‑1 (MQ=255)                                                                                                atgatCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGc                                         <  4:210269/136‑1 (MQ=255)                                                                                                atgatCACGGCGGGGGCGGTGTACGGGCCAGACGTGTCACACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGc                                         <  5:265530/136‑1 (MQ=255)                                                                                                 tgatCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGcc                                        <  6:269181/136‑1 (MQ=255)                                                                                                      aCGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCg                                    <  3:41761/135‑1 (MQ=255)                                                                                                           ggggTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATa                               >  4:212741/1‑135 (MQ=255)                                                                                                                  gggtACGGGCCAGACGTGTCACACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTgc                       <  1:185511/134‑1 (MQ=255)                                                                                                                     tACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTgcgc                     >  5:144440/1‑135 (MQ=255)                                                                                                                            cAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCgg             <  3:172968/136‑1 (MQ=255)                                                                                                                              gACGTGTCATACACCAGCACCGGGGCGGTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGa           <  4:33200/136‑1 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGaca                                                            <  8:199835/85‑1 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGaca                                                            >  7:199835/1‑85 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGCGCCTTCGACATACACCTTGCGCGAAAGCGGGAAc         >  7:279850/1‑136 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGCCATCCACCTTGCGCGAACGCGGGAAc         >  2:281188/1‑136 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAAc         >  8:243590/1‑136 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAAc         >  8:19421/1‑136 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAAc         >  8:279180/1‑136 (MQ=255)                                                                                                                                cGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAAc         >  8:130024/1‑136 (MQ=255)                                                                                                                                  tgtCACACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGATCCTTCGACATACACCTTGCGCGAACGCGGGAACgg       >  4:9244/1‑136 (MQ=255)                                                                                                                                    tCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGt      <  7:142223/135‑1 (MQ=255)                                                                                                                                      aTACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTg    >  6:236890/1‑135 (MQ=255)                                                                                                                                       tACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACTCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATAAACCTTGCGCGACCGCGGGAACGGTTGCa  >  8:139390/1‑136 (MQ=255)                                                                                                                                       tACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTGCa  >  2:281541/1‑136 (MQ=255)                                                                                                                                       tACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTGCa  >  2:162121/1‑136 (MQ=255)                                                                                                                                       tACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTGCa  >  4:140062/1‑136 (MQ=255)                                                                                                                                       tACACCAGCACCGGGGCGTTGGACTCGCCGCAGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTGCa  >  4:69834/1‑136 (MQ=255)                                                                                                                                       |                                                                                                                                        GACCGAAGTCGGAGCTCAGGCCTTCCAGGCGCTCGGTGTCACCGCGGGCTTCGATCCACGCCGAACGCACATCGGGCAGGCCTTTGCGCACGTCGATGATCACGTCGGGGTCGGTGTACGGGCCAGACGTGTCATACACCAGCACCGGGGCGTTGGACTCGCCGCCGAAATCGGTCGGGGTGTCATCCAGGCTGATTTCACGCATGGGGACACGGATGTCCGGGCGCGAGCCTTCGACATACACCTTGCGCGAACGCGGGAACGGTTGCA  >  ACB143/5592936‑5593205

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑