Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	518,393	T→C	13.7%	intergenic (+107/‑324)	ybbP → / → rhsD	putative ABC transporter permease/Rhs family putative polymorphic toxin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	518,393	0	T	C	13.7%	70.6 / 2.9	29	intergenic (+107/‑324)	ybbP/rhsD	putative ABC transporter permease/Rhs family putative polymorphic toxin
Reads supporting (aligned to +/- strand):  ref base T (17/8);  new base C (2/2);  total (19/10)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

TGGTTAAGGGTAAGGCGCTGTTCAGGCAGTTTGCGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAATTTGTTGATGATGAATTCATCT  >  CP009273/518246‑518536                                                                                                                                                    |                                                                                                                                                tGGTTAAGGGTAAGGCGCTGTTCAGGCAGTTTGCGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTAAGGATGTTATTGAATTGGTGATTTCCTATCTTTCTa                                                                                                                                                >  2:120219/1‑149 (MQ=255)                cgcTGTTCAGGCAGTTTGCGGGGTGATGAGAGTAAATAAGGGGCGTACTAGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATAAGTTTCATTGATGATGTTATTGAATGGGTGATTTCCTATCCTTCTATTGCTGGTaataata                                                                                                                                 >  2:193157/1‑148 (MQ=255)                 gcTGTTCAGGCAGTTTGCGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCt                                                                                                                                >  2:191755/1‑149 (MQ=255)                      tCAGGCAGTTTGCGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATc                                                                                                                                 <  1:23939/143‑1 (MQ=255)                                tGCGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGttt                                                                                                                 >  2:259331/1‑149 (MQ=255)                                  cGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTAt                                                                                                               <  2:57225/149‑1 (MQ=255)                                  cGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGGTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTAt                                                                                                               >  2:431403/1‑149 (MQ=255)                                        gatgaGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAACTTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGAttt                                                                                                         <  2:316132/149‑1 (MQ=255)                                                        gggCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCCATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGc                                                                                               >  1:7021/1‑143 (MQ=255)                                                        gggCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCCATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGc                                                                                               >  1:7182/1‑143 (MQ=255)                                                                  gTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATATCCCTACAAAAATAACTc                                                                               >  2:187611/1‑149 (MQ=255)                                                                   ttGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCa                                                                              >  2:70146/1‑149 (MQ=255)                                                                              gCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGAGGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAAACGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATaaaa                                                                   <  2:175602/149‑1 (MQ=255)                                                                                     ttAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAaaat                                                                  <  1:168809/143‑1 (MQ=255)                                                                                          ttaattCTACAATATGGTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAaatcataaatcata                                                       >  2:276057/1‑149 (MQ=255)                                                                                                    aaTATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACGAATAAAATCATAAATCATATGCg                                                   >  1:114619/1‑143 (MQ=255)                                                                                                     atatGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATg                                            <  2:27331/149‑1 (MQ=255)                                                                                                            tCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCCTAAATCATATGCGTTGAATGGAtatta                                     >  2:196250/1‑149 (MQ=255)                                                                                                                  atgatgTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCata                               >  2:272548/1‑149 (MQ=255)                                                                                                                  atgatgTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAACAACTCAGACTACCAAAATCATAACTCCCATGCGTTGAACGGAcatta                                     <  1:51831/143‑1 (MQ=255)                                                                                                                      tgTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCa                                 >  1:382458/1‑143 (MQ=255)                                                                                                                          aTTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCAAtata                             >  1:327871/1‑143 (MQ=255)                                                                                                                                ttGGTGATTTCCTATCTTTCTATTGCTGCTATTAATCTGAATCGGTGGAGTTTATTGATTTTCAATTTAGCCCTCCAAAAATAACTCAGATTAATAAAATCATAAATCATATGCGTTGAATGGATCTTATCCATATAGTGAAt                       >  1:87736/1‑143 (MQ=255)                                                                                                                                    tGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAATttgt                   >  1:73533/1‑143 (MQ=255)                                                                                                                                    tGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAATTTGTtgatga             <  2:168362/149‑1 (MQ=255)                                                                                                                                    tGATTTCCTATCTTTCCATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAATTTGTtgatga             <  2:8199/149‑1 (MQ=255)                                                                                                                                    tGATTTCCTATCTTTCCATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAATTTGTtgatga             <  2:8389/149‑1 (MQ=255)                                                                                                                                         tCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAAGTTGTtgatg              >  1:73306/1‑143 (MQ=255)                                                                                                                                               cTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTCGAATGGTTTTTATCCATATAGTGAATTTGTTGATGATGAATTCATCt  >  2:188917/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                TGGTTAAGGGTAAGGCGCTGTTCAGGCAGTTTGCGGGGTGATGAGAGTAAATAAGGGGCGTTCTGGTTGAATGGAACGCCTTGTTTAAATTAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTCCTATCTTTCTATTGCTGATATTAATCTGAATCGGTGGAGTTTATTGATTTTAAATATAGCCCTACAAAAATAACTCAGACTAATAAAATCATAAATCATATGCGTTGAATGGATATTATCCATATAGTGAATTTGTTGATGATGAATTCATCT  >  CP009273/518246‑518536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑