Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_vch_tpiA3,288,0330TG20.0% 63.5 / 10.1 30intergenic (+23/‑57)yraH/yraIputative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base T (12/12);  new base G (2/4);  total (14/16)
Fisher's exact test for biased strand distribution p-value = 6.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CCAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAGGCGCTTGCAGGAGGAATCGTTTTACAGC  >  NC_000913_3_vch_tpiA/3287895‑3288177
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ccAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATAAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGTATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATAAc                                                                                                                                        <  1:188538/149‑1 (MQ=255)
 cgaTGTTATTGGCAATTTTGACCTCATAATTTACTACGTATCAAACGTAGTTCCAGCAGAACTGCCCCCCGGGGAAGCAGATGCTATCGTTAACGGTACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACg                                                                                                                                       <  2:83236/147‑1 (MQ=255)
    tGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTGATACGTTAGGGCGTTATCTGACCTGTCAGATAACGccc                                                                                                                                    >  1:466835/1‑149 (MQ=255)
        aTTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGCCAGATAACGCCCtttt                                                                                                                                >  1:166668/1‑149 (MQ=255)
             cAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTttccttc                                                                                                                           <  1:332845/149‑1 (MQ=255)
             ataTGTTGACCGCGTCGTTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTttccttc                                                                                                                           <  2:29979/147‑1 (MQ=255)
              aaTGTTGACCTCATCGCTTACTACGTATCAACCGAAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTttccttcc                                                                                                                          <  2:467967/149‑1 (MQ=255)
                tGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCctc                                                                                                                        <  2:466835/149‑1 (MQ=255)
                       cTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTCACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCACATAACGCCCTTTTCCTTCCTCTTTCTCg                                                                                                                 >  2:255018/1‑149 (MQ=255)
                         cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGtt                                                                                                               <  1:222000/149‑1 (MQ=255)
                             gCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGa                                                                                                                                            >  2:480511/1‑116 (MQ=255)
                             gCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGa                                                                                                                                            <  1:480511/116‑1 (MQ=255)
                                   tacGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGtt                                                                                                     >  2:172688/1‑149 (MQ=255)
                                            aCCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATaa                                                                                            >  1:205419/1‑149 (MQ=255)
                                            aCCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATaa                                                                                            <  1:172688/149‑1 (MQ=255)
                                             ccGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATAAc                                                                                                                                        <  2:483754/104‑1 (MQ=255)
                                             ccGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATAAc                                                                                                                                        >  1:483754/1‑104 (MQ=255)
                                                                cACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATaa                                                                                                                                         >  1:445186/1‑84 (MQ=255)
                                                                cACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATaa                                                                                                                                         <  2:445186/84‑1 (MQ=255)
                                                                   cccAGGGGAAGGAGACGCTATTGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTcgcg                                                                     <  2:181931/149‑1 (MQ=255)
                                                                   cccAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTCGGGCGTTATCTGACCTGTCAGATAACGCCCTTGTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAACCGCACATTcgcg                                                                     >  1:20104/1‑149 (MQ=255)
                                                                   cccAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTcgcg                                                                     >  1:170403/1‑149 (MQ=255)
                                                                       gggtAAGCAGACGCCTTCGTTACCGTAACGCTGGAGTATCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAATGACCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGa                                                                 <  2:264523/149‑1 (MQ=255)
                                                                               aGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAAcc                                                         >  1:25880/1‑149 (MQ=255)
                                                                                   gCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCttgt                                                     >  1:360778/1‑149 (MQ=255)
                                                                                        tgTTAACGTACCACTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTgtgt                                                <  2:488585/148‑1 (MQ=255)
                                                                                                    gCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTAtt                                    <  2:170403/149‑1 (MQ=255)
                                                                                                                            ggCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAGCGGCTTGCaggagaacca            >  1:465333/1‑144 (MQ=255)
                                                                                                                                     tGACCTGTCAGATAGCGGCCTTTTCCTTCCTCTTTCTCGTTTTATCAGGTTGAAAAATAACGATGTCAAAAAGAACATTCGCGGTGATATTATCATTGTTGTGTAGCTTTTGTATTGGGCAGTCGCTGGCAGGCGGAATCGTTTTACAg   >  2:449772/1‑149 (MQ=255)
                                                                                                                                      gACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGGGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAGGCGCTTGCAGGAGGAATCGTTTTACAGc  <  1:118953/149‑1 (MQ=255)
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CCAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAGGCGCTTGCAGGAGGAATCGTTTTACAGC  >  NC_000913_3_vch_tpiA/3287895‑3288177

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑