Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi3,708,4290TC22.6% 48.8 / 13.0 31intergenic (‑724/+187)dppA/proKdipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro
Reads supporting (aligned to +/- strand):  ref base T (9/15);  new base C (5/2);  total (14/17)
Fisher's exact test for biased strand distribution p-value = 1.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.25e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ATAAGGCGGTCGCGCCGCATCCGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCA  >  NC_000913_3_pae_pgi/3708281‑3708575
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aTAAGGCGGTCGCGCCGCATACGATAATGGCCGGCAAATTTGCCTGATGCGACGCTGAGGCTTCTTATCAGGGCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCATCATGAGCTGCAGATGCAAAAAAGCCTGCTCGtt                                                                                                                                                    >  2:354733/1‑149 (MQ=25)
    ggCGGTCGCGCCGCATCCGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGc                                                                                                                                                <  1:169967/149‑1 (MQ=255)
         tCGCGCCGCATCCGACAATGGCCGGCACATTTGCCAGCTCCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCCTCCTCATGAGCTGCAGATGCAAACACGCCTGCTCGTTGAGCCGGCt                                                                                                                                           >  1:378221/1‑149 (MQ=25)
               cgcATCCGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGTCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCAACGAGCAGGCttttt                                                                                                                                       <  2:93306/147‑2 (MQ=25)
               cgcATCCGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGTCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCAACGAGCAGGCttttt                                                                                                                                       >  1:93306/1‑146 (MQ=255)
                   tCCGACAATGGCCTGTACATTTGCTTGATGCGACGCTGACGCGTCTTATCAGGCCGACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTAATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAAttt                                                                                                                                 <  2:114681/149‑1 (MQ=21)
                     cGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTgg                                                                                                                               >  1:271009/1‑149 (MQ=255)
                     cGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATATgg                                                                                                                               >  1:51904/1‑149 (MQ=255)
                     cGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCAACGAGCAgg                                                                                                                                             >  2:176643/1‑135 (MQ=255)
                       aCAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTGCGCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTc                                                                                                                             <  1:187386/149‑1 (MQ=255)
                                 gCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATagag                                                                                                                   <  2:79657/149‑1 (MQ=255)
                                   ataTTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGTGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGa                                                                                                                 <  2:32622/147‑1 (MQ=255)
                                     aTTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGAtt                                                                                                               <  1:32463/149‑1 (MQ=255)
                                         gCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTc                                                                                                           <  1:266861/149‑1 (MQ=255)
                                         gCCTGATGCGACGCTGAAGCGTCTTAGGGAGCCTACGTCGAGTCGACCCTCCCTGTCACCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTc                                                                                                           <  2:76603/149‑1 (MQ=17)
                                                        gACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTc                                                                                            <  1:390452/149‑1 (MQ=255)
                                                                       gCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTTGCCCTGCGGGCCGtt                                                                             >  1:264690/1‑149 (MQ=255)
                                                                                gagtcgaACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAAGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCCCCACTTCGCGGCTGGCCCTGACGAAGGTTGCTCGCGCa                                                                    >  2:426626/1‑149 (MQ=14)
                                                                                          tCCCTGCCCTCGGAGGTTCGCGTCCTCATGAGCTGCAGATGCAAAAAAGTCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTtctctc                                                          <  2:263421/149‑1 (MQ=255)
                                                                                          tCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCATATCCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTACAGCCTTGCTTTTCGGGCCGTTGCTGGCGCAACGTtctctc                                                          <  1:354733/149‑1 (MQ=17)
                                                                                          tCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTtctctc                                                          <  1:295923/149‑1 (MQ=255)
                                                                                                   ccGGAGGTTCTCATCCTCATGGGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTc                                                 <  1:315406/149‑1 (MQ=255)
                                                                                                                tCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTcc                                    <  1:79306/149‑1 (MQ=255)
                                                                                                                tCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTcc                                    >  2:79306/1‑149 (MQ=255)
                                                                                                                                aTGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGACCCTCCCTGCCCCCGGCAGTtc                    >  1:362189/1‑149 (MQ=255)
                                                                                                                                    aaaaaaGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTCCCTGccc                              <  1:83902/135‑1 (MQ=255)
                                                                                                                                    aaaaaaGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTCCCTGccc                              >  2:83902/1‑135 (MQ=255)
                                                                                                                                      aaaaGCCTGCTCAACGAGCAGGCTTCTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTcc                                    <  1:140485/127‑1 (MQ=38)
                                                                                                                                      aaaaGCCTGCTCAACGAGCAGGCTTCTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTcc                                    >  2:140485/1‑127 (MQ=38)
                                                                                                                                         aGCCTGCTCAACGAGCAGGCTTTTTGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCa           >  1:377568/1‑149 (MQ=39)
                                                                                                                                          gCCTGCTCAACGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCTGCGTTCTCTCGCTTCGCTCGGGTCGAACCTCCCTGCCCCCGGAGGGTCTCATCCTCAt          >  1:273834/1‑149 (MQ=38)
                                                                                                                                                  gTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACTTCCCTGCCCCACGATCGCCTCATCCTCAagagatcgc  >  2:369505/1‑144 (MQ=38)
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ATAAGGCGGTCGCGCCGCATCCGACAATGGCCGGCACATTTGCCTGATGCGACGCTGACGCGTCTTATCAGGCCTACGTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCAGATGCAAAAAAGCCTGCTCGTTGAGCAGGCTTTTCGAATTTGGTCGGTGATAGAGGATTACTCGCCACTTCGTGGCTCGCCCTGCGGGCCGTTGCTGGCGCAACGTTCTCTCGCTTCGCTCGAGTCGAACCTCCCTGCCCCCGGAGGTTCTCATCCTCATGAGCTGCA  >  NC_000913_3_pae_pgi/3708281‑3708575

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: ‑