Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	46.5%	62.0 / 18.2	43	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (21/2);  new base C (0/20);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 2.62e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATG  >  NC_000913/1376355‑1376643                                                                                                                                                            |                                                                                                                                            cGCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAaca                                                                                                                                             <  1:82012/151‑1 (MQ=255)      aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCt                                                                                                                                         <  2:318256/150‑1 (MQ=255)       ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCg                                                                                                                                       >  1:142757/1‑151 (MQ=255)           cgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                    >  1:609998/1‑150 (MQ=255)                    cgccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCccgc                                                                                                                           <  1:632763/149‑1 (MQ=255)                     gccgcGTAGCCTGGACGGCGCCCGCAAAATGGCGAGTGATTCCCTGCGCGCACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑CGCCCGCCGt                                                                                                                        >  2:686958/1‑151 (MQ=255)                             gCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACAtcgt                                                                                                                >  1:265195/1‑151 (MQ=255)                             gCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCACTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACAtcgt                                                                                                                >  2:475373/1‑151 (MQ=255)                                 ggACGGCGACGGCAAAAGGGGGAGTGTTCCCCTGCGCGTCCTGG‑AACAGGTCGCCGCGCGTCCCGAAA‑CC‑GG‑GGTTTACCTCGACCCGTAAAC‑CCGCTATCAGGATCATATGATCACCCCCCCCCCCGA‑TGCCCGCCGTTACATCGTCGaa                                                                                                            <  1:280689/151‑1 (MQ=255)                                 ggACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGa                                                                                                             >  1:222963/1‑150 (MQ=255)                                     ggCGACCGCAAAATGGTGGGTGATTCCCGGCGCGTACTGG‑AACAGGTCGCCGCGCTTCCCGAAC‑CC‑GT‑GGTGTATCTCAACCCGTAAAC‑CCTCTATCAGGATAATATAATCAACCCCCTCGCCGA‑TGCCCGCCGTTACATCGTCGaaaa                                                                                                          <  1:65693/149‑1 (MQ=255)                                          ccGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                   >  1:835162/1‑151 (MQ=255)                                             aaaaaggtttagtgtTTCCCTCGGCGTCCGGA‑ACCGGGCCCCCGCCCGTCCCGTAC‑CG‑GT‑GTGGTACCTCAACCTGTAAAC‑CCGTTATCAGGATAATATAAACACCCCCCCCGCGGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTaaa                                                                                                <  2:854740/141‑1 (MQ=255)                                              aaatgggTGAGTGATTCCCGGCGCGTACGGG‑AACGGGTCGCCGCGCGTGCCGGAA‑CG‑GG‑GGTGTTTCTCAAACCTTAAAC‑CCGCTATCAGGATAATATAACAACCCCCCCCCCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                 <  1:709938/144‑1 (MQ=255)                                                    gggagtgtTCCCCTGCGCTTACGGA‑AACGGGCCGCCGCGCGTCCGGGAC‑CC‑GG‑GGTGTATC‑CCAACCCTTAAACCCGTTATCAGGATCATAGAAACAACCCCCTCGCCGA‑GGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                         <  2:218889/149‑1 (MQ=255)                                                        gtgaTTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                         >  1:287741/1‑147 (MQ=255)                                                          gcttCCCTGCGCGT‑CTGGAAAAAGGTCGCCGCGCGCCCCGGAC‑CC‑TG‑GGGGTTTCCGGAACCTTAAAA‑CCGCTAAAAGGAATTTAGGAGCACCCCCCCCCCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                    <  1:467807/148‑1 (MQ=255)                                                            tccccTGCGCGTACGGA‑AAAGGGTCGCCGCGCG‑ACCGGGA‑CCTGT‑GGTGTATC‑CCAACCCTTAAACCCTCTATCAGGATAATATGACCACCCCCCCCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                    <  2:580767/146‑1 (MQ=255)                                                              cccTGGGCGTTCTGA‑AACGGGCCGCCGCGC‑TTCCGGAAGCT‑GT‑GGTGTA‑CCCCAACCGTTAAACCCGCTATCGGGATCATATAATAAACCCCCT‑GTCGATTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                 <  1:736172/149‑1 (MQ=255)                                                               ccTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                              >  2:872742/1‑151 (MQ=255)                                                                    gcgTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                         >  2:260876/1‑151 (MQ=255)                                                                      ttatggg‑AACGGGCCGCCGCGCGTCCCGGAC‑CC‑GT‑GTTTTATCCCGAACCGTTAAC‑CCTTTACAAGGATAATATAATCACCCCCCTCGCGGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                          <  2:753406/143‑1 (MQ=255)                                                                           gg‑AACAGGTCGCCGCGCGTCCCGGAA‑CG‑GG‑GTTGTATCTCAACCCGTAAAC‑CCTCTATCAGGATCATATGATCAACCCCCCCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTa                                                                      <  2:890717/147‑1 (MQ=255)                                                                              aaCAGGCCCCCGCGCGTA‑CGGAA‑CC‑GTGGGTGTACCTCAACCCGTAAAC‑CCCCTATAAGGATAATATAACCACCCCCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTAt                                                                     <  2:192334/146‑1 (MQ=255)                                                                                 aGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                              >  1:431283/1‑150 (MQ=255)                                                                                 aGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                              >  1:760987/1‑150 (MQ=255)                                                                                  ggTCCCCGCGCGTCCCGAAC‑CC‑GT‑GGTGTATCTCGACCCGTAAAC‑CCGCTACCAGAATCATATGATCAACCCCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                             <  1:440742/150‑1 (MQ=255)                                                                                      gccgcGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                        >  1:18236/1‑151 (MQ=255)                                                                                        cgcgcgTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                       >  1:284989/1‑150 (MQ=255)                                                                                            cgTACCGGAC‑CG‑GT‑GGTGTATCTCGACCCGTTAAC‑CCGCTATCAGGATAATATGACCAACCCCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaagaa                                                   <  1:539780/150‑1 (MQ=255)                                                                                             gTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                    >  2:943435/1‑148 (MQ=255)                                                                                                ccGGAC‑CG‑GT‑GGTGTATCTCGAACCGTTAAC‑CCGTTATCAGGATCATATGATCAACCCCCTCGCCGT‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                              <  2:930821/151‑1 (MQ=255)                                                                                                accgAA‑CCGGT‑GTTGTATCCCGAACCGTTAAC‑CCGCTACCAGGATCATATGACCAACCCCCCCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                    <  2:427906/143‑1 (MQ=255)                                                                                                             ggttTATCCCGACCCGTTAAC‑CCGCTATCAGGATCATATGACCACCCCCCCCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                      <  1:903077/149‑1 (MQ=255)                                                                                                                gtATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcg                                 >  2:497018/1‑151 (MQ=255)                                                                                                                  taccccgaCCCTTAAACCCGCTACCAGGATCATATAATCAACCCCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcg                                 <  2:582899/143‑1 (MQ=255)                                                                                                                    ctcaacccttaaaa‑CCGCTACAAGGAAAATATAACCACCCCCCTCCCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgc                                  <  2:25662/135‑1 (MQ=255)                                                                                                                    cccaaaCCGTTAAC‑CCGTTATCAGGATAATATGATCAACCCCCGCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                             <  2:287514/147‑1 (MQ=255)                                                                                                                             ttAAC‑CCGCTATCAGGATCATATGATAACCCCCCCCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACaa                      <  1:420477/149‑1 (MQ=255)                                                                                                                             ttAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                    >  2:588149/1‑151 (MQ=255)                                                                                                                                           aGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg       >  2:400491/1‑151 (MQ=255)                                                                                                                                             gATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc     >  1:39685/1‑151 (MQ=255)                                                                                                                                                cATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg  >  2:497319/1‑151 (MQ=255)                                                                                                                                                cATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg  >  1:472774/1‑151 (MQ=255)                                                                                                                                                            |                                                                                                                                            CGCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAA‑CC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGA‑TGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATG  >  NC_000913/1376355‑1376643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑