Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	51.7%	35.2 / 43.6	29	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (0/14);  new base G (15/0);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.29e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-07

GTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTT  >  NC_000913/1097442‑1097724                                                                                                                                             |                                                                                                                                                  gTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAAccccc                                                                                                                                        <  2:125148/151‑1 (MQ=25)      cGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAAGGGGGGGGTTCAAAcccccatac                                                                                                                                    >  2:462338/1‑147 (MQ=255)                        gTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACt                                                                                                                 <  2:687393/150‑1 (MQ=255)                           gCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTcc                                                                                                             <  1:163295/151‑1 (MQ=255)                                 tGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCg                                                                                                        <  2:631615/150‑1 (MQ=255)                                         cccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTc                                                                                               <  1:417483/151‑1 (MQ=255)                                         cccGGTCGGGGCTTCTCAGCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTc                                                                                               <  2:488582/151‑1 (MQ=255)                                          ccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGATCGGAACCCCCCTACG‑TTTCCGGATACACACTTTCCCGGCGTg                                                                                                      >  2:579528/1‑143 (MQ=14)                                          ccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTc                                                                                               <  1:542025/150‑1 (MQ=255)                                              tCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGTTCGTACCCCCCCTACG‑TTGCCGTATACACACCTTTCAGGCGTGCTCCTTCCGcc                                                                                           >  1:122478/1‑150 (MQ=18)                                                   gCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGTTTGCAACCCCCATACG‑CTGCCGTTTACACACTTTTCACGCGGGCTCCTTCAGCCAc                                                                                         >  2:608474/1‑147 (MQ=17)                                                        tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGTTTGAACCCCCCCTACG‑TTGCCGTATACACACTTTTCAGGCGTGGTCCTTCCGCCCCC‑CGGGCAcc                                                                               >  1:447100/1‑151 (MQ=17)                                                          aTCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑GGGGGGGGGTTCGTAACCCCGGTACG‑TTGTCGTATACAAACTTTCTAGGCGTGGTCCTTCAGCCACT‑CCGACACCTc                                                                             >  1:601114/1‑151 (MQ=17)                                                           tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGGTCGAACCCCCGCTACG‑TTGCCGTATAAACACTTTTCACGCGGGGCCCTTCAGCCCCT‑CGGACACCTc                                                                             >  1:85204/1‑150 (MQ=17)                                                                 cGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGTTTGGAACCCCCCTACG‑TTTCCGTATACACACTTTCCCGGGGGGCCCCTTCAGCCACC‑CCGGCAccccccccaa                                                                       >  1:578950/1‑142 (MQ=14)                                                                    tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGATTGAAACCCCGCCACGCTTTCCCT‑TACACACTTTTCTGGCGGGCTCCTTCCGCCCCT‑CCGCCAccccccccaaattt                                                                   >  1:456398/1‑139 (MQ=2)                                                                         gCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGTTCGAACCCCCGATACG‑TTGCCGTATACACACTTTTCAGGCGGGCTCCTTCAGCCACT‑CGGGCACCCCACCAAATTTTCGtt                                                               >  1:188916/1‑150 (MQ=14)                                                                               taCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGGTCGAACACCCCCCTCG‑ATGCCCTATATACACTTTTCAGGCGGGCGCCCTCACCCCCC‑CGCCCACCTCACCAAAATGTTGTTCCtttt                                                         >  2:389056/1‑147 (MQ=2)                                                                                    aaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGGTTCTAACCCCCCCCACC‑TTTTCCGATACACACCTTTCAAGCGGGCTCCCTCCGCCCCC‑CCGGCACCCCCCCCAATTTTTGTTTCTGTCtt                                                       >  2:177882/1‑147 (MQ=2)                                                                                    aaaaaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTg                                                   <  2:401512/151‑1 (MQ=255)                                                                                         aaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACg                                              <  2:156398/151‑1 (MQ=255)                                                                                                     tCGTACGAGCTCTTCTTTAAATATGGCGGGG‑CGGGGGGGGGTTTGACCCCCCAACCC‑TTTCCGTATACACACCTTTCAGGCGGGGTCCCTCAGCCACT‑CCGGCACCTCCCCCAAATTTCGTTTCTGTCTTTTTGGAACGGGGGCTCAttt                                   >  2:599283/1‑150 (MQ=9)                                                                                                        tACGAGCTCTTCTTTAAATATGGCGGTG‑GGGGGGGGGGTCGGAACCCCCATACG‑GTTCCGTTTACAAACTTTTCCGGCGTGCTCCCTTAGCCACC‑CCGGCCCCCCACCAAAATTTTGTTTCCGTTTTTTTGGGACGGGGGCTTATTTAggg                               >  1:269838/1‑151 (MQ=2)                                                                                                                cttcttTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCa                         <  1:448296/149‑1 (MQ=255)                                                                                                                     ttAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCt                   <  1:39474/150‑1 (MQ=255)                                                                                                                       aaaTATGGCGGTG‑AGGGGGGGGTTCGAACCCCCCCTACG‑TTTCCGTATACAAAATTTCCAGGCGTGCTCCTTCTACCAATCCGGCCACC‑CACCCAAATGTCGTTCCTGTCTTTCTGGAAAGGGCGCTAATTTTGGGGAAACATg                       >  1:182280/1‑144 (MQ=12)                                                                                                                           atGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTc             <  1:609497/150‑1 (MQ=255)                                                                                                                                     aGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACttt   <  2:447059/151‑1 (MQ=255)                                                                                                                                      gggggggATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtttt  <  1:331239/151‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                  GTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTG‑AGGGGGGGATTCGAACCCCCGATACG‑TTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACT‑CGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTT  >  NC_000913/1097442‑1097724

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑