Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	659,942	0	G	A	51.3%	16.8 / 45.6	39	A92V (GCT→GTT)	lipA	lipoate synthase
Reads supporting (aligned to +/- strand):  ref base G (3/16);  new base A (20/0);  total (23/16)
Fisher's exact test for biased strand distribution p-value = 2.57e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-07

GGTCATCACGGTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCGCTGGA  >  NC_000913/659796‑660082                                                                                                                                                   |                                                                                                                                             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                                                           <  1:217066/151‑1 (MQ=255)                                                                                aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  1:46179/151‑1 (MQ=255)                                                                                aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  2:114095/151‑1 (MQ=255)                                                                                aTTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGc                                                           <  1:496633/151‑1 (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)                                                                                                                                                   |                                                                                                                                             GGTCATCACGGTCAACGGAGGTGATAACCACATAACGCAGCGCCATATCGGCAATGGTCTGCGCCAGTTTCACTGGTTCATTGGCATCAGGAGCTACCGGGCGACCGTGGGCAACATCACAGAACGGACAACGGCGGGTACAAATAGCGCCGAGGATCATAAACGTTGCTGTGCCGTGGTTGAAGCATTCCGCCAGGTTAGGGCAGGAGGCTTCCTCGCAGACAGAATGCAGGCCATTTTTGCGCATTGCGGCTTTGATGCCCTGGATACGTGTAGAGTCCGCTGGA  >  NC_000913/659796‑660082

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: ‑