Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,423,297	0	G	C	50.0%	44.3 / 24.5	38	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
Reads supporting (aligned to +/- strand):  ref base G (2/17);  new base C (19/0);  total (21/17)
Fisher's exact test for biased strand distribution p-value = 1.19e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTAC  >  NC_000913/3423150‑3423441                                                                                                                                                     |                                                                                                                                                   aaaTCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGc                                                                                                                                                 <  1:134030/151‑1 (MQ=255) aaaTCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTT‑CCCCCCCCCCCCCggg                                                                                                                                                  >  2:496781/1‑150 (MQ=255)       gagCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCGCCCCCCCCCCCCCCCGGCCGttt                                                                                                                                            >  1:464048/1‑150 (MQ=37)         gCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCG‑CCCCCCCCCCCCCCGGCCGGTGttt                                                                                                                                         >  2:758514/1‑151 (MQ=255)           gTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTT‑CCCCCCCCCCCCCCGGGCGTTGCTTc                                                                                                                                        >  2:180741/1‑150 (MQ=37)            tACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCG‑CCCCCCCCCCCCCCGGCCGTTGCtttg                                                                                                                                       >  2:477231/1‑148 (MQ=255)                aGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCG‑CCCCCCACCCCCCCCGCCGCTGCTTTTC‑AAc                                                                                                                                  >  1:756537/1‑150 (MQ=255)                 gggCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCG‑CCCCCCCCCCCCCCCGCCGTTgtctctcaca                                                                                                                                   >  1:86280/1‑140 (MQ=255)                       ttttATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTT‑CCCCCCCCCCTCCCGGCCCGTGCTTCTC‑AACGTTCAAAt                                                                                                                          >  1:587777/1‑151 (MQ=25)                        tttATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATc                                                                                                                         <  2:792122/151‑1 (MQ=255)                        tttATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATc                                                                                                                         <  2:393774/151‑1 (MQ=255)                         ttATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATcc                                                                                                                        <  2:602174/151‑1 (MQ=255)                                  gTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCCG‑CCCCCCCCCCCCCCGGCCGGTGCTTTGC‑AACCTTTCAATcccccccccg                                                                                                                >  2:408849/1‑148 (MQ=21)                                       ccATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGAtt                                                                                                          <  1:27425/151‑1 (MQ=255)                                       ccATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCCCCCCCCCCCCGGCCGCTGCTTTGC‑CAAGTTTAAAATCGCCCCccgcggggt                                                                                                          >  2:772102/1‑148 (MQ=18)                                            aaTTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTcc                                                                                                     <  2:647097/151‑1 (MQ=255)                                             aTTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATTGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCCCCACCCCCCCGGGCGGTTCTTCGC‑AAAGATTAAAACCCCCCCCGGCGGGGTTGTc                                                                                                      >  2:538078/1‑149 (MQ=18)                                                gAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTT‑CCCGCCACCCCCCCGGGCGTTTCTTTGC‑AAACTTATAATCCCCTCCCCGCGGGGTTGTCCtt                                                                                                   >  2:651382/1‑148 (MQ=255)                                                  aTGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCC‑CCCCCCACCCCCCCGGGCGCTGTTTTCT‑AAAAATCAAAATCGCTCCccgcgggattttgcttctc                                                                                                >  2:612013/1‑137 (MQ=12)                                                     ttAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGGCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCCCCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCggg                                                                                            <  1:424333/150‑1 (MQ=255)                                                      tAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGgag                                                                                          <  1:496543/151‑1 (MQ=255)                                                                  cAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCCCCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCAcc                                                                                <  2:634788/149‑1 (MQ=255)                                                                  cAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCAcc                                                                                <  2:392186/149‑1 (MQ=255)                                                                              ccgtcaggATGGCCTTCTGCTTAATTTGATGCCTGGCAGTTTATGGCGGGCTGCCTT‑ACCCCCCCCCCCCCTGCCCTTGCTTTTC‑AATCGTCAAATTCTCTTCCCGCGGTCTTTTTTTA‑CCCCCGAGAGTGTTCTCCGCCCTacaacac                                                                    >  1:199758/7‑148 (MQ=0)                                                                              ccTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTT‑CCCCCCCCCCCCCCGGCCGGTGCTTCCC‑CACCTTCAAAACCCCCCCCCGCGGGTTTTTCCTA‑CTCCGGAGGGGGTTTACCCacaaaaaaaaaaa                                                                  >  2:552307/1‑146 (MQ=9)                                                                                         gCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCCC‑CCCCCCCCCCCCCCGGCCGGTGCTTTGC‑AAAGGTCAAATCCCCCCCCCGCGGGGTTTTTCTT‑CTCCGGGGGGGGGTCACCCCCaaaaaaaaaaaaaaaaaaaaag                                                       >  2:352581/1‑149 (MQ=9)                                                                                          ccTTTCGCTTGATTTGATGTCGGGCAGTTTATGGCGGGCGCCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGc                                                      <  1:403578/151‑1 (MQ=255)                                                                                                    gatttgatGTCTGGCAGTTTATGGCGGGCGCCCTG‑CCCCCCACCCCCCGGGCCGCTGCTTTGC‑AACGTTCAAAACCCCCCCCCGCGGGTTTTTCCTT‑CTCCGGAGAGGGTTTACCCACAAAAAAAAGAAAAAAAAAAAAGCCCCGGCTTc                                             >  2:87560/1‑150 (MQ=255)                                                                                                     atttgatGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCCCCCCCCCGGCCGGTGCTTCGC‑CAACTTTAAATCCCCTACCCGCGGGGTTGTTCTC‑CTCCGGCGGGTGTTCACCCACAAAACAAAGATAAAAAAAAAAGCCCCGttcttcg                                           >  2:148155/1‑145 (MQ=2)                                                                                                     atttgatGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCCCCCCCCCCCCGGCCGGTGCTTCTCAAAGGTTCAAACCGCCCCCCGGCGG‑TTTGTCCTACCCCGGGGGGGGGTTCCCGAACAAACAACAAAAAAAACAAAAGACCCCGCCTTc                                             >  1:317514/1‑150 (MQ=2)                                                                                                     atttgatGTCTGGCAGTTTATGGCGGGCGGCCCG‑CCCCCCCCCCCCCCGGCCCGTGCTTTGC‑AAAGGTTAAATTCCCTCCCCGCGGGTTTTTCCTT‑CTCCGGGGAGGGTTTACCCCCAAACAACAGAAAAAAAAAAAAAGCCAGGCTTcc                                            >  2:523413/1‑150 (MQ=255)                                                                                                       ttgatGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGAc                                         <  1:792889/151‑1 (MQ=38)                                                                                                         gatGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCCCCCCCCCCCCGGCCGGTGCTTCGC‑CACCCTCCAATCCGCCCCCCGCCGGTTTTTCCTA‑CTCCGGGGGGTGGTCACCCACCAACAACAAATAAAAAAAAAAGCCCACTCCTCCggccg                                       >  1:237480/1‑147 (MQ=2)                                                                                                                     tttATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGt                             <  2:393855/149‑1 (MQ=38)                                                                                                                           gcgggcgTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTAttt                      <  1:500565/150‑1 (MQ=38)                                                                                                                               gcgTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATg                  <  2:566356/150‑1 (MQ=38)                                                                                                                                            ccACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTcc      >  2:655523/1‑150 (MQ=40)                                                                                                                                               ccccccGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTAc  <  2:320956/151‑1 (MQ=255)                                                                                                                                               cccTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTAc  <  1:180700/151‑1 (MQ=40)                                                                                                                                                     |                                                                                                                                                   AAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTG‑CCCGCCACCCTCCGGGCCGTTGCTTCGC‑AACGTTCAAATCCGCTCCCGGCGGATTTGTCCTA‑CTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTAC  >  NC_000913/3423150‑3423441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑