Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,466,255	C→A	65.0%	pseudogene (1482/3497 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,466,255	0	C	A	65.0%	13.6 / 21.0	31	pseudogene (1482/3497 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base C (5/6);  new base A (12/8);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 4.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.25e-01

TGGCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCG  >  CP009273/1466112‑1466396                                                                                                                                                |                                                                                                                                              tGGCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGGcc                                                                                                                                          >  1:99776/1‑149 (MQ=255) tGGCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGGGCACATCAACAAGTcc                                                                                                                                          >  1:2478/1‑149 (MQ=255)        tAACGAAGCACCCTGGAACCTCGGAAGTAGTAGTGAGGTTCACAAACCCCGGATACTGGAAGTTAATAATAATCCAGCCCTCAATAACCCCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGc                                                                                                                                   <  2:20125/149‑1 (MQ=255)            gAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACTACAAGAATGCTTTGCACATCAACAAGTCCGGTACGCTTta                                                                                                                               >  1:203233/1‑149 (MQ=255)                   cctggaacctCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATAcc                                                                                                                        <  2:463671/149‑1 (MQ=255)                   cctggaacctCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACAACTTATAATAcc                                                                                                                        >  1:2180/1‑149 (MQ=255)                    ctggaacctCGGAAGGAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTAAATAACCGCGGCGAGTTTATTCTGGATGCCGACAATAATTCTGTGAACAACAAAAAGTCCGGTACGCTTTGTAATACCg                                                                                                                       >  1:64139/1‑149 (MQ=255)                        aaccgCGGAAGCAGTAGCGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAATTCCGGTACGCTTTATAATACCGGTca                                                                                                                   <  2:102210/149‑1 (MQ=255)                          cctGGGAAGTAGTAGCGATGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGCGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTcacc                                                                                                                 <  2:239042/149‑2 (MQ=255)                            tCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATg                                                                                                               >  2:220407/1‑149 (MQ=255)                                aaGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACGTCAACCAGTCCGGTACGCTTTATAATACCGGTCACGTGACCa                                                                                                           >  1:155656/1‑149 (MQ=255)                                aaGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTAGGCTTTATAATACCGGTCACATGAACa                                                                                                           >  1:189044/1‑149 (MQ=255)                                aaGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGGCACATGAACa                                                                                                           >  1:155815/1‑149 (MQ=255)                                     gtagtGAGGGTAACAACACCGGGATGCTGGAAGTGAATAATAGTTCTGCTTTCAATAACCGCGGCGGGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATCCAGGTCACATGACCATCAGt                                                                                                      >  1:94005/1‑149 (MQ=255)                                          gAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAAttc                                                                                                 >  1:337819/1‑149 (MQ=255)                                                        cGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAg                                                                                   <  1:105034/149‑1 (MQ=255)                                                               cTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTaa                                                                            >  2:318950/1‑149 (MQ=255)                                                                tGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAat                                                                           <  1:406399/149‑1 (MQ=255)                                                                      ttAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTAGAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTgg                                                                     <  2:2478/149‑1 (MQ=255)                                                                       taataataaTTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTggg                                                                    >  1:129268/1‑149 (MQ=255)                                                                           aataatTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCgg                                                                >  2:328336/1‑149 (MQ=255)                                                                                       ttCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGttt                                                    <  2:287624/149‑1 (MQ=255)                                                                                          caTAACCGCGGCGAGTTTATTCTGGATAACGACAAGAATTGTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTAt                                                 <  2:41956/148‑1 (MQ=255)                                                                                          aaTAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTAt                                                 <  1:220407/149‑1 (MQ=255)                                                                                            tAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCGGTGCACATCAACAAGTCCGGTACGCTTTACAATACCGGTCCCATGAACACCAGTAATACTCCCCACCACGGAGACGTTAATCCGCGGGGCGGAAATGCTCGTCtcatca                                               >  2:124253/1‑149 (MQ=255)                                                                                                         tttATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGCGCCGTTAATATGTGGGGCGGAAAGGGTCGTTTTATCAATGACGGAACGAt                                  >  2:175714/1‑149 (MQ=255)                                                                                                                ttGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGtt                           >  1:40248/1‑149 (MQ=255)                                                                                                                        gACAAGAATTCTGTTCACATCAACAAGTCCGGTACGTTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGaa                   <  2:255453/149‑1 (MQ=255)                                                                                                                                  cTGTGGACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTa         <  1:220384/149‑1 (MQ=255)                                                                                                                                      gCACATCAACAAGTCCGGTACGTTTTATAATTCCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCa     <  2:189960/149‑1 (MQ=255)                                                                                                                                         caTCAACCCGTCCGGTACGCTTTATAATCCCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTGCTGCGAAGTCACTGGTAGTCAgcg  <  1:41906/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                              TGGCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCG  >  CP009273/1466112‑1466396

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑