Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	5,162	0	T	A	40.0%	42.1 / 17.5	42	intergenic (+142/‑72)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base T (14/10);  new base A (0/16);  total (14/28)
Fisher's exact test for biased strand distribution p-value = 1.07e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

ATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAAT  >  NC_000913/5013‑5310                                                                                                                                                       |                                                                                                                                                     atcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATa                                                                                                                                                     <  1:645057/151‑1 (MQ=255) atcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATa                                                                                                                                                     <  2:689046/151‑1 (MQ=255)        aaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAAccg                                                                                                                                              <  2:506696/151‑1 (MQ=255)               ttCATTATCTCAATCGGGCGGGGTTTGTTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAAAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTtc                                                                                                                                        <  2:390267/150‑1 (MQ=255)               ttCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTtct                                                                                                                                       >  2:322925/1‑151 (MQ=255)                                gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAGAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCgg                                                                                                                      >  1:769893/1‑151 (MQ=255)                                             ttATGCAGCCCTGCTTTTTTAGGAAGAAATTAGGGAAAAAAATGAAAGGGAAAAAGGAAAATTTCTAAATAAATGGGGTAATTT‑AGAGATAAGGAGTGCGGAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCAt                                                                                                          <  1:518186/150‑1 (MQ=255)                                                     ccgggtttttttATAAAAAAATTAGGGAAAAAAATGACAGGAAAAAAGGAAAAATTCTAAAAAAAGGGGGTAACTT‑AGAGATTGGGTTGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                                                                                 <  1:121897/145‑1 (MQ=255)                                                     cccGGTTTTTTTATGAAAAAATTATGGAAAAAAATGACAGGGAAAAAGGAGAAATTCTAAAAAAAGGCGATAATTT‑AGAGATTAGGATTGCGAAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                                   <  1:307923/149‑1 (MQ=255)                                                     cccGGTTTTTTTAAAAAAAAATTGGGGAAAAAAAGGACAGGAAAAAAGGAAAAATTCTAAATAAATGCGTTAATTT‑AGAGATTAGGAGTGCGGGAAAAAACAGCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCaa                                                                                                 <  2:765015/151‑1 (MQ=255)                                                        ggCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                               >  1:122950/1‑150 (MQ=255)                                                         gttttttaaaaaaaaaaTTATGGAGAAAAAGGAAAGGAAAAAAGAAGAAATCCAAAAAAAATGGGTTAACTA‑AGAGATAAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGa                                                                                              <  2:117441/136‑1 (MQ=255)                                                           tttttaaaaaaaaaaTTAGGGAAAAAAAGGAAAGGAAAAAAGGAAAAATTCCAAATAATGGGGTTAACTT‑GGAGATTGGGAGGGGGGAAAACACAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGa                                                                                              <  2:513707/136‑1 (MQ=255)                                                           tttttaATGAAAAAATAAGGGAAAAAAATGACAGGAAAAAAGGAAAAATTCACAAAAAAGGGGGTAATTT‑AGAGATAGGGATTGCGGAAAACAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATg                                                                                               <  2:237824/147‑1 (MQ=255)                                                            tttttATAAAAAAATAATGGAAAAAAATGAGAGAAAAAAAGAAAAAATCCAAAAAAAGTGCGGTATCTT‑AGAGATTAGGAGGGAGAAAAATAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaa                                                                                           <  2:727540/150‑1 (MQ=255)                                                                       aaaTTAGGAAAAAAAATGACAGGGAAAAAGGAAAAATTCTAAATAAATGCGGTAACTT‑AGAGATTAGGATTGGGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAcc                                                                                <  1:81326/150‑1 (MQ=255)                                                                              gaaaaaaaaTGACAGGAAAAAAGGAAAAATTCTAAAAAAAGGGGTTAACTT‑AGAGATTAGGATTGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                            <  1:399907/143‑1 (MQ=255)                                                                                aaaaaaaTGACAGGAAAAAAGGAAAAATTCT‑AAAAAATGGCGTAAATTAAGAGATTAGGTTGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAg                                                                      <  1:334266/149‑1 (MQ=255)                                                                                 gaAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAGTCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                        >  2:188717/1‑148 (MQ=255)                                                                                      aTGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCa                                                                 >  1:244084/1‑150 (MQ=255)                                                                                           ggggAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAt                                                           >  1:613489/2‑151 (MQ=255)                                                                                           aGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAt                                                           >  1:158184/1‑151 (MQ=255)                                                                                            ggaaaaaaGGAAAAATTCAAAAAAAAGGCGGTAACTT‑AGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                            <  2:345666/146‑1 (MQ=255)                                                                                            ggaaaaaaGGAAAAATCCTAAAAAAAGGCGGTAACTA‑AAAGATTAGGATGGGGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAAt                                                               <  2:210594/143‑1 (MQ=255)                                                                                               aaaaaGGAAAAATTCTCAAAAATTGCGTTAACTT‑AGATATTAGGATGGCGGAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGt                                                        <  2:94455/150‑1 (MQ=255)                                                                                               aaaaaGGAAAAATTCACAAAAAATGCGGTAACTT‑AGAAATAAGGATGGAGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTa                                                            <  2:725266/146‑1 (MQ=255)                                                                                                     gagaAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGc                                                  >  2:389952/1‑150 (MQ=255)                                                                                                      agaAATTCTAAAAAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCAc                                                <  1:476032/151‑1 (MQ=255)                                                                                                        aaaTTCTAAATAAATGCGTTAATTT‑AGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCAc                                                <  1:38427/149‑1 (MQ=255)                                                                                                        aaaTTCTAAAAAAATGCGGTAATTT‑AGAGATTAGGATGGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACt                                               <  1:534104/150‑1 (MQ=255)                                                                                                               cAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTgg                                       >  1:562623/1‑151 (MQ=255)                                                                                                                 aaaaaTGCGGTAATTT‑AGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                         <  2:538852/145‑1 (MQ=255)                                                                                                                 aaaaaGGCGGTAACTT‑AGAGATAAGTATTGCGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTccc                                          <  2:429799/144‑1 (MQ=255)                                                                                                                 aTAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCAGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGtt                                     >  2:754936/1‑151 (MQ=255)                                                                                                                     aTGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTgg                                 >  1:491325/1‑151 (MQ=255)                                                                                                                          gTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCt                            >  1:625159/1‑151 (MQ=255)                                                                                                                                        tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgcagca                >  2:439833/1‑150 (MQ=255)                                                                                                                                          ggatggggaaaaaTAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGgcagca                <  2:769525/137‑1 (MQ=255)                                                                                                                                                 ggAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAgg            <  1:207011/145‑1 (MQ=255)                                                                                                                                                 gaaaaaTAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTg         <  1:737427/144‑1 (MQ=255)                                                                                                                                                     aaTAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTg         <  2:31591/144‑1 (MQ=255)                                                                                                                                                     aaTAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAAt  >  2:351177/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                     ATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTT‑AGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAAT  >  NC_000913/5013‑5310

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑