Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,622,8720TC67.9% 81.3 / 48.3 81H391H (CAT→CAC) ppkpolyphosphate kinase, component of RNA degradosome
Reads supporting (aligned to +/- strand):  ref base T (0/26);  new base C (55/0);  total (55/26)
Fisher's exact test for biased strand distribution p-value = 8.83e-22
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AAAGATTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCGTGGTG  >  W3110S.gb/2622831‑2622896
                                         |                        
aaaGATTCCCGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1076589/1‑61 (MQ=255)
aaaGATTCACGCATCATCGCCTCGATGATCCCCGCCGCACACAACGGTAAGAAAGTCACCg       >  1:374558/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCAcc        >  1:57321/1‑60 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCAGCgt      >  1:1015148/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:836283/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1459984/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:927921/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:599825/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:418795/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:396868/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:991024/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1524595/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:368675/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1047025/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:367252/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:768155/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:16526/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:342528/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:651953/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:29356/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:740063/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:186675/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1443602/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1122333/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1178644/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:534987/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:505085/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1338203/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:502510/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1393092/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1394014/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCgt      >  1:1459857/1‑62 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:494107/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:485237/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:532103/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:478445/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:471277/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:545011/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1060491/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:657867/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:171333/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1043990/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1237698/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:988417/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1345730/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1428038/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1442810/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1481184/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1482482/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:857474/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:1619501/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:167962/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:761340/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCACCg       >  1:693966/1‑61 (MQ=255)
aaaGATTCACGCATCATCGACTCGATGATCCACGCCGCACACAACGGTAAGAAAGTCAACgt      >  1:95172/1‑62 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:892324/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:925108/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:936551/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:636336/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:970021/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:588981/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1025/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1614935/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1036030/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1256279/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:136234/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1391359/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1462139/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1474306/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1506355/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1553276/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:529746/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:168477/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:183166/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:219374/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:305232/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:360633/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:4599/62‑1 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtgggg  <  1:1296277/62‑3 (MQ=255)
    aTTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAACTCACCgtggtg  <  1:290024/62‑1 (MQ=255)
     ttCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCgtggtg  <  1:1644231/61‑1 (MQ=255)
                                         |                        
AAAGATTCACGCATCATCGACTCGATGATCCACGCCGCACATAACGGTAAGAAAGTCACCGTGGTG  >  W3110S.gb/2622831‑2622896

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