Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,278,095	0	C	G	28.3%	87.0 / 10.5	47	G66G (GGC→GGG)	ompA_1	Outer membrane protein A
Reads supporting (aligned to +/- strand):  ref base C (5/28);  new base G (13/0);  total (18/29)
Fisher's exact test for biased strand distribution p-value = 8.42e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCTACGCACAGCGATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGCCCACTGAAAC  >  KT2440/1277961‑1278228                                                                                                                                         |                                                                                                                                       gcTACGCACCTCACTGGCAGCGCGCCCCTCAATCAACGGACCGGGCCCAGCTGCCGCCTGCGGGGCGGCTGGGGCGGGGGGGGCGTGGGTGCCAGCGAGAGTTCTGCCTGGGCCGCCGGTGGG‑GGCGCCTTGGg‑cg‑c                                                                                                                                     <  6:52272/137‑1 (MQ=255)   tACGCACAGCGATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGTGGG‑GG‑ccc                                                                                                                                   >  2:53968/1‑136 (MQ=255)   tACGCACAGCGATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGGCGTGGG‑CG‑ccc                                                                                                                                   >  6:439585/1‑136 (MQ=255)         caGCGATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCcg                                                                                                                             <  5:382966/137‑1 (MQ=255)             gATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGGCGTGGG‑GGCCCATTG‑cggcgg                                                                                                                         >  5:361937/1‑137 (MQ=255)             gATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGTGGG‑GG‑CCCATGGcggcgg                                                                                                                         >  2:342924/1‑137 (MQ=255)             gATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGGTGG‑GG‑CCATTGGccgcgg                                                                                                                         >  1:122567/1‑137 (MQ=255)              aTGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCGTGTG‑GG‑CCAGTGACGGCggg                                                                                                                        >  6:351434/1‑137 (MQ=255)               tGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGTGGG‑CG‑CCATTTGCCGCgggg                                                                                                                       >  2:382852/1‑136 (MQ=255)                  cAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGTGGG‑GG‑GCCTTTGCGGCggggggg                                                                                                                    >  8:67310/1‑133 (MQ=255)                     cgcgcCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGAttt                                                                                                                 <  8:133648/137‑1 (MQ=255)                     cgcgcCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGAttt                                                                                                                 <  8:462654/137‑1 (MQ=255)                     cgcgcCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGGCGGGGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGAttt                                                                                                                 <  4:134178/137‑1 (MQ=255)                       cgcCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGGCGTGGG‑GG‑CCCGTTCCGGCGGGCGGGttttt                                                                                                               >  3:216126/1‑135 (MQ=255)                       cgcCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCGTTTGG‑GG‑CCAATGACGGCGGGCGGAgtttt                                                                                                               >  7:59286/1‑135 (MQ=255)                       cgcCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCGTGGG‑GG‑CCAATGGCGCCCGGCGGATTTGt                                                                                                               >  8:326290/1‑137 (MQ=255)                          cccTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGGGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTAc                                                                                                            <  1:378302/137‑1 (MQ=255)                                 acaaAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAgg                                                                                                     <  5:73377/136‑1 (MQ=255)                                  caaAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGa                                                                                                    <  7:326290/137‑1 (MQ=255)                                        aCCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCTTGGG‑CG‑GCAGAGCCGGCGGGCTGTTTTGTTTCAGCCAGGACgggtt                                                                                              >  8:445767/1‑134 (MQ=255)                                                     gCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGTGGG‑GG‑CCCTTGCCGGCGGGCGGATTTTTTTAGCCCCCGGCGGGGGCGGAGATGGTggg                                                                                 >  5:182911/1‑135 (MQ=255)                                                              tgGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCCTGGG‑GG‑CCCGTGGCCGCGGGGGGGTTTGTTTAGCCCCAGCCGGGGACGGAGCTTGTGACGGGAtgttt                                                                        >  3:294149/1‑136 (MQ=255)                                                                ggcggcTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGTGGGGGCGTGGGG‑GG‑CCATT‑CCGGGGGGGGGGGTTGTTTGGGCCCGGCCGGTGGCGAAGATGGTGGCGGGAgttttgt                                                                      >  8:34089/1‑134 (MQ=255)                                                                ggcggcTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGGCGTGGGCCG‑CCTTTG‑CGGCGGGGGGGTTTTTTTAGGCCACGGCCGTGGCGCAGAAGGTGAGCGCATTTTAGa                                                                      >  5:372703/1‑137 (MQ=255)                                                                  gggcTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGAcc                                                                    <  4:47811/136‑1 (MQ=255)                                                                          tCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGGGCCGTTGG‑GG‑CCAATGCCGGCGGGCTGATTTTTTTAGCCCCGCACGGTGGCGAATATTGTGTCGGCAATTTAGACCGGggcggg                                                            >  6:465086/1‑135 (MQ=255)                                                                           gggtgggtgCCTTGGTGCCATCGAGAGGTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATc                                                           <  8:337267/136‑1 (MQ=255)                                                                            ggtggtGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCa                                                          <  5:439585/137‑1 (MQ=255)                                                                            ggggggggCCTTGTGGCCAGCGAGAGTTCTTCCGGGGCCGCCGGTGGG‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCa                                                          <  2:229260/131‑1 (MQ=255)                                                                            ggggggggCCTGGGTGCCATCGAGAGTTCTTCGGGGGCCGCCGGGGGG‑GGCTCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCa                                                          <  2:254959/131‑1 (MQ=255)                                                                                 gggCCTTGGTGCCAGCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGcc                                                     <  4:107259/136‑1 (MQ=255)                                                                                            ccATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCGTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCg                                          <  8:363250/137‑1 (MQ=255)                                                                                                   gagTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGAAACGAGACCCCGGCCAaca                                   <  3:155142/137‑1 (MQ=255)                                                                                                       tcttcCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACAcggc                               <  1:342924/137‑1 (MQ=255)                                                                                                        gttcCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCGGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACAcggcg                              <  7:215365/136‑1 (MQ=255)                                                                                                        cttcCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACAcggcg                              <  7:231829/137‑1 (MQ=255)                                                                                                        cttcCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACAcggcg                              <  4:34880/137‑1 (MQ=255)                                                                                                           ccTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCTGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACTTCATTTTAGACCTTATATATCAATTCCCCGAGACCCCGGCCAACACGGCGGtt                           <  8:59286/137‑1 (MQ=255)                                                                                                                gccgcgGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCAGAGACCCCGGCCAACACGGCGGTTGACca                      <  6:372703/137‑1 (MQ=255)                                                                                                                      ggtggt‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATggg                <  1:53968/137‑1 (MQ=255)                                                                                                                        gggt‑ggCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCt              <  2:346523/136‑1 (MQ=255)                                                                                                                          gt‑ggCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGc            <  2:149540/137‑1 (MQ=255)                                                                                                                           t‑ggCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGcc           <  7:34089/137‑1 (MQ=255)                                                                                                                            gggCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGcc           <  1:199256/136‑1 (MQ=255)                                                                                                                            gggCGCCTTGGG‑AG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGcc           <  4:294149/136‑1 (MQ=255)                                                                                                                             ggCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGccc          <  1:74805/137‑1 (MQ=255)                                                                                                                                 ccTTGGG‑CG‑CCATTGCCGGAGGGCTGATTTGTTACGCCCAGGACGGTGACGACTATTGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGCCCACTg      <  6:300862/137‑1 (MQ=255)                                                                                                                                     ggg‑CG‑CCAATTCCGGCGGGGTGATTTTTTTAGCCCAGGACGGGGACGAAGATGGTGACGGCATTTTAGACCCGCGCGATCACTGCCCCGCGACCCCCGCCAACACCGCGGTTGACCACAATGGCTGCCCACAGaaaa  >  2:74805/1‑136 (MQ=255)                                                                                                                                         |                                                                                                                                       GCTACGCACAGCGATGGCAGCGCGCCCCTCAATCAAAGGACCTGGCCCATCTGCAGCCTGCTGGGCGGCTTGGTCGGTGGTGGCCTTGGTGCCATCGAGAGTTCTTCCTGGGCCGCCGGTGGT‑GGCGCCTTGGG‑CG‑CCATTGCCGGCGGGCTGATTTGTTACGCCCAGGACGGTGACGAAGATGGTGACGGCATTTTCGACCGGCGCGATCACTGCCCCGAGACCCCGGCCAACACGGCGGTTGACCACATGGGCTGCCCACTGAAAC  >  KT2440/1277961‑1278228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑