Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	659,940	0	T	A	47.5%	45.1 / 16.5	40	I93F (ATT→TTT)	lipA	lipoate synthase
Reads supporting (aligned to +/- strand):  ref base T (5/16);  new base A (19/0);  total (24/16)
Fisher's exact test for biased strand distribution p-value = 3.39e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCGCAGGTCATCACGGTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCGCTGGA  >  NC_000913/659790‑660082                                                                                                                                                       |                                                                                                                                               cgcgCAGGTCATCACGGTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAAt                                                                                                                                                <  1:21037/151‑1 (MQ=255)       ggTCATCACGGTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAacgc                                                                                                                                           >  1:83617/1‑150 (MQ=255)                ggTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAAGGCCGGGGagaat                                                                                                                                 >  1:408653/1‑147 (MQ=255)                    aaCGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAAc                                                                                                                             <  2:44899/151‑1 (MQ=255)                     aCGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGGCCAAAAGCGGCGAGGAGCATAAAca                                                                                                                            >  1:530522/1‑150 (MQ=255)                          ggTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAAAGCCGAGGGACATAAAAGtgggt                                                                                                                       >  2:37536/1‑147 (MQ=255)                               tAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATTAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCGAGGGACATAAACGGTGCTGTGc                                                                                                                   >  2:194388/1‑150 (MQ=255)                                  ccACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTAAAAAAAACGCCCAGGGTCATAAAAGTTGCTGTGCCggg                                                                                                               >  2:448970/1‑149 (MQ=255)                                  ccACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGGAAAATAACGCCGGGGAAGATAAAACATTCTGTGCCggg                                                                                                               >  1:471163/1‑149 (MQ=255)                                  ccACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCGAGGATCATAAAAGTTGCTGTGCCggg                                                                                                               >  2:77007/1‑149 (MQ=255)                                                  cATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGcc                                                                                               <  2:378923/151‑1 (MQ=255)                                                   atatCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAACGGCGGGGATCATAAAAGTTGGTGTGTCGGGGGTGGAGAATTCcccc                                                                                               >  1:239842/1‑150 (MQ=255)                                                   atatCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAAAGCCGGGGGACATAAAAGTTGTTTTGCCGGGGGTGTAGCATTCcccc                                                                                               >  1:302235/1‑150 (MQ=255)                                                    tatCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTGCAAAAAAAGCCGGGGAACCTAAACATTGCTGTGCCGCGGTTGGAgaaatacccca                                                                                              >  1:407117/1‑140 (MQ=255)                                                       cGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGtt                                                                                          <  2:402755/151‑1 (MQ=255)                                                          cAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAgg                                                                                       <  1:55716/151‑1 (MQ=255)                                                              ggTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCGCGGAACATAAAAGTTGCTGTGCCGTGGGTGAAGCATTCCGCCCGGGTAGGGCag                                                                                   >  2:536577/1‑151 (MQ=255)                                                                 cTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCaggag                                                                                <  2:172392/151‑1 (MQ=255)                                                                   gcgcCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACCAAAAACGCCCGGGAGCATAAAAAGTGCTGTGCCGTGGGTGAAGGATTTCGCCCGGGTAGGGGagggggg                                                                              >  1:198684/1‑150 (MQ=255)                                                                      ccAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTc                                                                           <  2:16187/151‑1 (MQ=255)                                                                        aGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGATCAAAAACGCCCAGGAGCCTAAAAGCTGCTGTGACCTGGGTGTAGAATTTCCCCCGGGTATGGGagggggggtcc                                                                          >  2:170677/1‑145 (MQ=255)                                                                          tttCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCGGGGGGCATAAAAGTTGGTGTGCCGGGGGTGGAGCAATACCCCCGGGTAAGGGAGGAGGGGTCCTc                                                                        >  1:489680/1‑150 (MQ=255)                                                                                 ggTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCCGGGGTCATAAACGTTGATGTGCCGCGGGTGGAGCATTCCGCCAGGGTAGGGGAGGGGGCGTCCTCGccgaccg                                                                >  1:304673/1‑149 (MQ=255)                                                                                 ggTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCCGGGGTCATAAAAGTTGCTGTGCCGGGGGTGGAGCATTTCGCCCGGGTAGGGGAGGGGGGTTCCTCGccgacaa                                                                >  2:265474/1‑150 (MQ=255)                                                                                      aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  2:114095/151‑1 (MQ=255)                                                                                      aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  1:496633/151‑1 (MQ=255)                                                                                      aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  1:46179/151‑1 (MQ=255)                                                                                      aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  1:217066/151‑1 (MQ=255)                                                                                           cATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTAAAAATAAAGCCCAGGGATATAAAACTTGCTTGGGCGTGGTTGAAAAATTTCGCCCGGGTAGGGCAGGAGGGTTCCCCGCCGACCAAAAGCAggg                                                       >  2:342361/1‑149 (MQ=255)                                                                                           cATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCGAGGAACATAAAAGGTGCTGTGCCGGGGGTGGAGCAATCCGCCCGGGTTGGGGAGGGGGGGTCCTCGCCGACAGAATGCAggg                                                       >  2:120125/1‑149 (MQ=255)                                                                                           cATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAAAGCCGAGGATCATAAAAAGTGCTGTGGCGGGGGTGAAGCATTTCCCCCGGGTAGGGCAGGGGGGTTCCTCGCCGACAGAAAGCAGGc                                                       >  2:323678/1‑150 (MQ=255)                                                                                                               ccGTGGGCAACATCACAGAACGGACAACGGCGGGGACAAAAAACGCCGAGGATCATAAAAGTTGCTGTGGCGTGGGTGAAGCATTCCGCCCGGGTAAGGGAGGAGGGTTCCTCGCCGACAGAAAGCAGGGCCTTTTTTCGCATTGCGGGtt                                  >  2:71245/1‑151 (MQ=255)                                                                                                                 gTGGGCAACATCACAGAACGGACAACGGCGGGTACAAAAAACGCCGGGGATCATAAAACTTGCTGTGCCGGGGGTGAAGCATTCCGCCCGGGTAGGGGAGGGGGGGTCCTCGCAGACAAAATGCAGGCCCTTTTTTTGCATTGGGGCtttt                                >  1:309944/1‑150 (MQ=255)                                                                                                                       aaCATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGccc                          <  2:489690/151‑1 (MQ=255)                                                                                                                                 aaCGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATa                    <  2:40783/147‑1 (MQ=255)                                                                                                                                 aaCGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATa                    <  2:424514/147‑1 (MQ=255)                                                                                                                                 aaCGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACgtg                <  2:120038/151‑1 (MQ=255)                                                                                                                                         aCGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTcc        <  1:11452/151‑1 (MQ=255)                                                                                                                                           ggcggGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCg       >  2:167620/1‑150 (MQ=255)                                                                                                                                               ggTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCGCTgg   <  1:345950/150‑1 (MQ=255)                                                                                                                                               ggTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCGCTGGa  >  2:190534/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                               CGCGCAGGTCATCACGGTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCGCTGGA  >  NC_000913/659790‑660082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑