Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	164,620	C→T	11.8%	intergenic (+86/‑110)	hrpB → / → mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	164,620	0	C	T	11.8%	99.4 / 6.9	45	intergenic (+86/‑110)	hrpB/mrcB	putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
Reads supporting (aligned to +/- strand):  ref base C (16/22);  new base T (2/3);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.73e-02

ATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCAAAGG  >  NC_000913/164473‑164767                                                                                                                                                      |                                                                                                                                                    aTGTCTGGCCGGACGACCCCGCACACACCGCACCGACGCGACGGCCGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCCCCCTCACCCGCACCCCCTCCCTCa                                                                                                                                                    >  2:285225/1‑149 (MQ=37)    tCTGGCCGGACGGCCGGGCAAATTCTGCACCGGCGCGACGGACGAAAAGGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAgg                                                                                                                                                 <  2:194003/149‑1 (MQ=38)      tGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCCAgggg                                                                                                                                               >  2:20516/1‑148 (MQ=255)           tgacgacCCGGCAAATACTGTACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAggg                                                                                                                                          <  1:713412/148‑1 (MQ=255)            gacgacCCGGCAAATACTGCACCGACGCGACGGCCGACAGCGACTGCGTTGGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTTGAGGGAGAgggt                                                                                                                                         <  1:256476/149‑2 (MQ=25)            gacgacCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTTGAGGGAGAgggt                                                                                                                                         <  1:730827/149‑2 (MQ=255)            gacgacCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTTGAGGGAGAgggt                                                                                                                                         <  1:71960/149‑2 (MQ=255)              cgacCCGGCAAATACGGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGAc                                                                                                                                       <  1:453473/149‑1 (MQ=255)               gacCCCGCAAATACTGCTCCGACGCGACAGACGAAAAAGTCTTCGTAAGGTCGGTTT‑‑TCTCCCTCTCCCGGGCGGCGTGGGACGTGGCGCGGGCATCAGCGCGCACGTTCACCCGCCCCCTAACCCCACCCCGCAAGGGCAAGGGGccc                                                                                                                                      >  2:38030/1‑149 (MQ=255)                  ccGGCAAATACTGCCCCGTCGCGACGGCCGAACAAGTATTCGTAAGGTTGGTTT‑‑CCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGAt                                                                                                                                   <  1:53945/149‑1 (MQ=38)                  ccGGCAAAGGCTGCACCGTCTCGTCGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCATCTCTCACTTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGAt                                                                                                                                   <  1:463195/149‑1 (MQ=37)                   cGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCCCCCTCAAGGGAGAGGGGACCGATc                                                                                                                                  >  1:236337/1‑149 (MQ=255)                               cACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAAt                                                                                                                        <  1:45088/149‑1 (MQ=255)                                 ccGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTg                                                                                                                    >  1:51656/1‑149 (MQ=255)                                              cgAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGGGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGCCCGATCGAGCACAAAGTTTGAGAGATAtcttct                                                                                                       >  2:325597/1‑149 (MQ=255)                                                 aaaaGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCCAGCACAAATTTTGAGAGATAtcttcttct                                                                                                    >  2:503800/1‑149 (MQ=255)                                                                 ttggttT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACagaaga                                                                                    <  2:728880/149‑1 (MQ=255)                                                                   tgttT‑‑TCCCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAAc                                                                                  <  1:361041/148‑1 (MQ=255)                                                                   ggttT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAAc                                                                                  <  1:2924/149‑1 (MQ=255)                                                                              cctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCg                                                                         <  2:87767/149‑1 (MQ=255)                                                                              cctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCg                                                                         >  1:41071/1‑149 (MQ=255)                                                                              cctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGATGACGCTCACCCTAACCCTCTCCCTCACGGGAGGGGGGACCGATCGAGCGCAAATTTTGAGAGTTATCTTCTTCTGTCTTCTAAGAGCAGAACCGAACATCg                                                                         >  1:51292/1‑149 (MQ=37)                                                                                    cctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGCACAGAAAAGCGGGCgtt                                                                   <  2:600301/149‑1 (MQ=255)                                                                                      tgtgGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGGCCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTg                                                                 >  2:421714/1‑149 (MQ=255)                                                                                      tgtgGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTg                                                                 >  1:464908/1‑149 (MQ=255)                                                                                                ggCCGGGGTGAGGGCATCAGCGCGCACGTCCCCCCCACCCCTAAGCCGCTGCCTCAAGGGAGAGGGGACCGATCGAGCACAAATCTTGAGACATATCCTCTTCCGCCTTGTAACAGAAGCACAGAACATCCGGCTTTTGCGACtccatc                                                       <  2:748512/149‑6 (MQ=255)                                                                                                ggCCGGCGGGAGCGCATCAGCGCGCACGTTCACCCTCACCCTAACCCGCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGCAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAata                                                       <  2:49048/149‑1 (MQ=255)                                                                                                  ccGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATAtt                                                     >  2:590472/1‑149 (MQ=255)                                                                                                     gggTGCGGGCCTCAGCGCGCACGTGCACCCTCACCCTAACCCGCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGGCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCg                                                  <  1:484482/149‑1 (MQ=255)                                                                                                     gggTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCCCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCg                                                  <  1:20516/149‑1 (MQ=255)                                                                                                       gTGAGGGCAGCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGga                                                <  1:98399/149‑1 (MQ=255)                                                                                                       gTGACGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGga                                                <  2:570322/149‑1 (MQ=255)                                                                                                             gCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGaaaaa                                          <  2:602038/149‑1 (MQ=255)                                                                                                             gCATCAGCGCGCAAGTTCACCCTCACCCTAACCCTCTCCCTAAAGGGAGGGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGaaaaa                                          >  1:560870/1‑149 (MQ=255)                                                                                                                   gcgcgcACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATgg                                    >  1:703716/1‑149 (MQ=255)                                                                                                                     gcgcACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAGAAGCATGGcc                                  >  1:476570/1‑149 (MQ=255)                                                                                                                         aCGTTCACCCTCACCCTAACCCTCTCCCTGAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAAGAGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGa                              >  1:550536/1‑149 (MQ=255)                                                                                                                                         gtccccTCTCCCTTGAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAAt              >  2:749540/4‑149 (MQ=255)                                                                                                                                            cccTCTCCCTTGAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTgg           >  2:741740/1‑149 (MQ=255)                                                                                                                                                 tcCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGCCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCa      <  1:279947/149‑1 (MQ=255)                                                                                                                                                  cccTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCaa     >  2:101587/1‑149 (MQ=255)                                                                                                                                                    cTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATACCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGAGAGCCAATTGGACGCAAAg   <  1:310439/149‑1 (MQ=255)                                                                                                                                                     tCAGGGGAGAGGGGGCCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCGTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCAAAgg  <  2:309417/149‑1 (MQ=255)                                                                                                                                                     tCAAGGGAGAGGGGACCGATCGAGCCAAACTGTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCAAAgg  >  1:777073/1‑149 (MQ=255)                                                                                                                                                     tCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCAAAgg  <  2:747523/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    ATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTT‑‑TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTTTGCGCCTGAATATTGCGGAGAAAAAGCATGGCCGGGAATGACCGCGAGCCAATTGGACGCAAAGG  >  NC_000913/164473‑164767

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑