Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,629,125	C→A	14.1%	L309I (CTT→ATT)	yhiM →	acid resistance protein, inner membrane

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,629,125	0	C	A	14.1%	124.3 / 3.0	42	L309I (CTT→ATT)	yhiM	acid resistance protein, inner membrane
Reads supporting (aligned to +/- strand):  ref base C (17/19);  new base A (3/3);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.81e-01

ACTGGCTGTGGTGTTATTGGGTTATTTTTCTCGGCTCAATCACGGTACTGCAGGGGATATACGTCTTAGTCAGTTCCGATGCAAGCGCCCGACTGGCTCCCGGCATTATTCTTATTTGCCTCGGAATGATCTGTTACAGCATATTCTCAAAAGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTACCGGATAAAACCAGCGTTGACCATTTGCGTAACGCTGGTTTTTCTTAGGCATCATGAAATAACGCAGCA  >  CP009273/3628868‑3629332                                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                acTGTCTTTGGTGTTATTGGGTTAATTTTCTCATACCAAGCACGGTACTGCAGTGTATATTCTTCTTCGTCAGTTCCGATGCAAGCGCCCGACTGGCTCCCGGCATTATTATTATTTTCCTCGGAATGATCTGTTACAGCATATTCTCCAAAGTCTGGCTACTGGCACTTGTATGGAGACGTACCTCTTACTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCGGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAg                                                                                                                                                                                                <  2:296854/275‑1 (MQ=255)                                                          tataCGTCTTAGTCAGTTCCGATGCAAGCGCCCGACTGGCTCCCGGCATTATTCTTATTTGCCTCGGAATGATCTGTTACAGCATATTCTCAAAAGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTa                                                                                                                                                                             >  1:143071/1‑237 (MQ=255)                                                                                                                            gatattgttGTTACATCATATTCTTAAAAGTTTGGCTACTGGTACTGGTATGGAGACGTACCTGTTCGTTAGACAACAGAATACCGATGATTCCCGACTACACCTGCCTGTTTTGCCTTTTCCTGGCATGGTTTCTGACGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTAc                                                                      <  1:351499/266‑1 (MQ=255)                                                                                                                                              tatTCTCAAAAGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTAGGt                                                                                                                                                      >  2:195668/1‑176 (MQ=255)                                                                                                                                                ttCTCAAAAGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTg                                                                                                                                                                                                              <  2:580107/118‑1 (MQ=255)                                                                                                                                                  ctcAAAAGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTAGGTTTgg                                                                                                                                                  <  1:195672/176‑1 (MQ=255)                                                                                                                                                      aaaGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGTCGCAGAcc                                                                                                                                                                                             >  1:556493/1‑129 (MQ=255)                                                                                                                                                          tCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGTCGCAGACCGACa                                                                                                                                                                                         <  2:556482/129‑1 (MQ=255)                                                                                                                                                                 aagggtcagggTATTGATACGTACTTTTTCTTTATCCAACGGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTACCGGATAAAACCAGCGTTGACCATTTGCGTAACGCTGGt                                <  1:353969/266‑1 (MQ=255)                                                                                                                                                                        cTGGTATGTAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTtc                                                                                                                           >  1:65370/1‑177 (MQ=255)                                                                                                                                                                            tATGTAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCaa                                                                                                                       <  2:65370/177‑1 (MQ=255)                                                                                                                                                                                     gTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAAt                                                                                                                                                                                                       >  1:198898/1‑88 (MQ=255)                                                                                                                                                                                     gTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAACACTAATTGCAACGTACCGGATAAAACCAGCGTTGACCATTTGCGTAACGCTGGATTTTCTTCGGCATCATGaaa            >  1:165695/1‑275 (MQ=255)                                                                                                                                                                                         cTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGgcg                                                                                                                                                                                                   <  2:198894/88‑1 (MQ=255)                                                                                                                                                                                            ttCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTc                                                                                                                                                              >  2:311911/1‑122 (MQ=255)                                                                                                                                                                                                ttAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGt                                                                                                                                                          <  1:311916/122‑1 (MQ=255)                                                                                                                                                                                                gtggCCAACAGAATACCGGTGAGGTCCGTCTGCACCTGCCTGGTTTGCCTTTGCCTTGTATCGTTGCTGGCGGAAAGGGCGCAGACCGACAGGGGATATTGTATTCCGTCGCGAGTGCTGGTCGGTTTGGGAGCGGTATGCGTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGGACCGGATAAAACCAGCGTTGACCATTGGCGTAACGCTGGTTTGGCTTAGGCATCATTAAAGAACgcagca  <  2:165692/271‑1 (MQ=255)                                                                                                                                                                                                      aaCAGAATACCGATGATTCCCGTCTTCACATGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTAGCGAGTTc                                                                                                                                                              >  2:331115/1‑112 (MQ=255)                                                                                                                                                                                                          gAATACCGATGATTCCCGTCTTCACATGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTAGCGAGTTCTGGt                                                                                                                                                          <  1:331120/112‑1 (MQ=255)                                                                                                                                                                                                                  atgatTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTATTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTAc                                                                      >  1:622713/1‑188 (MQ=255)                                                                                                                                                                                                                   tgatTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATgg                                                                                                                                                                                                     >  1:393565/1‑60 (MQ=255)                                                                                                                                                                                                                     atTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTcg                                                                                                                                                                     >  2:643200/1‑90 (MQ=255)                                                                                                                                                                                                                      ttCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTATTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTACCGGa                                                                  <  2:622702/188‑1 (MQ=255)                                                                                                                                                                                                                       tCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGgcgc                                                                                                                                                                                                  >  2:18234/1‑59 (MQ=255)                                                                                                                                                                                                                       tCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCa                                                                                                                                                                                                 <  2:393560/60‑1 (MQ=255)                                                                                                                                                                                                                         ccGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAg                                                                                                                                                                 <  1:643211/90‑1 (MQ=255)                                                                                                                                                                                                                           gTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGAc                                                                                                                                                                                              <  1:18234/59‑1 (MQ=255)                                                                                                                                                                                                                              ttCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTATTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTc                                                                                                                                                              >  2:575948/1‑88 (MQ=255)                                                                                                                                                                                                                                  cctgcctgTTTTGCCTTTTCCTGGCATCGTTTATTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGt                                                                                                                                                          <  1:575959/88‑1 (MQ=255)                                                                                                                                                                                                                                     gcctgTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGAcc                                                                                                                                                                                             >  2:233803/1‑50 (MQ=255)                                                                                                                                                                                                                                      cctgTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGACATGGCGCAGACCGACATGGGATCTTTTATTCCTTCGCGAGTTTTGGTCGGTTTGGGAGCGGTATGCtt                                                                                                                                     >  2:625264/1‑105 (MQ=255)                                                                                                                                                                                                                                      cctgTTTTGCCTTTTCCTGGCATCGTTTATTGCGGAAATGgcgc                                                                                                                                                                                                  >  1:315206/1‑44 (MQ=255)                                                                                                                                                                                                                                      cctgTTTTGCCTTTTACTGGCATTCTTTCATGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTACCGGATAAAACCAGCGNTGACCATTTGCGTAACGCTGGTTTTTCTTAGGCATCATGAAATAACgcag    >  1:467245/1‑234 (MQ=255)                                                                                                                                                                                                                                         gTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACa                                                                                                                                                                                         <  1:233807/50‑1 (MQ=255)                                                                                                                                                                                                                                          ttttGCCTTTTCCTGGCATCGTTTATTGCGGAAATGGCGCAGAc                                                                                                                                                                                              <  2:315201/44‑1 (MQ=255)                                                                                                                                                                                                                                          ttttGCCTTTTCCTGGCAGCGTTTCTGGCGGAAATGGCGCAGACCGACATGGGATATTTGATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACg                                                                                                                                 <  1:625275/105‑1 (MQ=255)                                                                                                                                                                                                                                                    tCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTa                                                                                                                                                                             >  2:599026/1‑51 (MQ=255)                                                                                                                                                                                                                                                        ggCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTcc                                                                                                                                                                         <  1:599037/51‑1 (MQ=255)                                                                                                                                                                                                                                                         gCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAg                                                                                                                                               >  1:99221/1‑76 (MQ=255)                                                                                                                                                                                                                                                         gCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCtt                                                                                                                                     >  2:281161/1‑86 (MQ=255)                                                                                                                                                                                                                                                             cGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGt                                                                                                                                           <  2:99221/76‑1 (MQ=255)                                                                                                                                                                                                                                                             cGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACg                                                                                                                                 <  1:281166/86‑1 (MQ=255)                                                                                                                                                                                                                                                                  cTTGCGGAAATGGCGCAGACTCACATGGGATATTTTATTACTTCGCGAGTTCTGGt                                                                                                                                                          <  1:452514/56‑1 (MQ=255)                                                                                                                                                                                                                                                                  cTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGt                                                                                                                                                      >  1:156554/1‑60 (MQ=255)                                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                ACTGGCTGTGGTGTTATTGGGTTATTTTTCTCGGCTCAATCACGGTACTGCAGGGGATATACGTCTTAGTCAGTTCCGATGCAAGCGCCCGACTGGCTCCCGGCATTATTCTTATTTGCCTCGGAATGATCTGTTACAGCATATTCTCAAAAGTCTGGCTACTGGCACTGGTATGGAGACGTACCTGTTCGTTAGCCAACAGAATACCGATGATTCCCGTCTTCACCTGCCTGTTTTGCCTTTTCCTGGCATCGTTTCTTGCGGAAATGGCGCAGACCGACATGGGATATTTTATTCCTTCGCGAGTTCTGGTCGGTTTGGGAGCGGTATGCTTTACGTTGTTCTCAATCGTTTCAATATTAGAAGCGGGTTCTGCTAAAAAATAATTGCAACGTACCGGATAAAACCAGCGTTGACCATTTGCGTAACGCTGGTTTTTCTTAGGCATCATGAAATAACGCAGCA  >  CP009273/3628868‑3629332

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑