Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,205	0	A	C	30.8%	67.3 / 11.0	39	S215R (AGT→AGG) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base A (26/1);  new base C (0/12);  total (26/13)
Fisher's exact test for biased strand distribution p-value = 3.32e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGA  >  NC_000913/3556066‑3556338                                                                                                                                              |                                                                                                                                      ccaccTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGaaaa‑a                                                                                                                                       >  2:828574/1‑140 (MQ=255) ccaccTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGaaaa‑a                                                                                                                                       >  1:469241/1‑140 (MQ=255)     cTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTTGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTcc                                                                                                                                   >  1:916119/1‑140 (MQ=255)         ccACTGACGCCTTTTTCCCCGACAACAAAAAAGCGTTCGGTGATTTTTCCCCTTTCGCCTCCAAGCGAGACGTTA‑TCCCCGGCCCCGTGGCCGCGCGGCGGGTTATGAATATTCTTTTCAGGCAGGAAAAA‑CCCCCCCGc                                                                                                                               <  2:469241/139‑1 (MQ=255)             tGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAgt                                                                                                                           >  1:213243/1‑140 (MQ=255)               aCGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAgtgt                                                                                                                         >  1:544027/1‑140 (MQ=255)                      tttCCCCGACGACAAAAAAGCGTTCGGTGATTTTTTCCTTTTCGACTTAAAGCGAGACGGTATTCCCCGCCCCC‑GGGGCGCGCGGCAGTTTATAAATTTTCTGTTCAGGGGGGAAAAA‑CCCCCCCGCCAGTGTAGCGAtt                                                                                                                  <  2:1434006/140‑1 (MQ=255)                             gacgaaAAAAAAGCGTTCGGTAATTTTTTCATTTTCGACTACAAGCGAGACGTTATTCCCCGCCCCC‑TGGCCGCGCGGCAGGTTATAAATTTTCTGTTCATGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCt                                                                                                           <  2:1198387/140‑1 (MQ=255)                                 acAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGc                                                                                                       >  1:117915/1‑140 (MQ=255)                                          cGTTCGGTGATTTTTTCACTTTCGACTTCAGGGGAGGCGTTATTCCCCGGCCCC‑GGGTCGCGGGGCAGGTTATGAATATTCTGTTCATGCGGGGAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgcg                                                                                              <  2:286283/140‑1 (MQ=255)                                               ggTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGca                                                                                         >  1:759346/1‑140 (MQ=255)                                                 tGATTTTTTCCCTTTCGTCTTCAAGCGAGACGTTATTCCCCGGCCCC‑TGGTCGCGCGGCAGGTTATAAATTTTCTGTTCAGGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGcaca                                                                                       <  2:916119/140‑1 (MQ=255)                                                            ttttCGACTACAAGGGAGACGTTATTCCCCGGCCCC‑TGGTCGCGCGGAAGTTTATAAATATTCTGTTCAGGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAg                                                                            <  2:1149326/139‑1 (MQ=255)                                                             tttCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGa                                                                           >  1:1406737/1‑140 (MQ=255)                                                                      cAAGGGAGACGGTATCCCCCGCCCCC‑TGGTCGCGCGGCAGTTTATAAATATTCTGTCCATGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCa                                                                  <  2:435072/140‑1 (MQ=255)                                                                           gagaCGTTATCCCCCGCCCCC‑TGGCCGCGCGGCAGTTTATAAATATTCTGTTCATGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCAt                                                             <  2:1020632/140‑1 (MQ=255)                                                                              gcGGTATTCCCCGCCCCC‑TGGCCGCGCGGGAGTTTATAAATTTTCTGTTCAGGGAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg                                                          <  2:384849/139‑1 (MQ=255)                                                                              cagttATTCCCCGCCCCC‑TGGTCGCGCGGCAGTTTATAAATATTCTGTTCATGAAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg                                                          <  2:840334/136‑1 (MQ=255)                                                                              aaggTATTCCCCGCCCCC‑TGGTCGCGGGGCAGGTTATGATTATTCTGTTCATGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg                                                          <  2:290014/138‑1 (MQ=255)                                                                               cGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGc                                                         >  1:1020632/1‑140 (MQ=255)                                                                                gttATTCCCCGGCCCC‑TGGTCGCGGGGCAGTTTATAAATTTTCTGTTCATGAAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGca                                                        <  2:1406737/138‑1 (MQ=255)                                                                                       cccGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGtt                                                 >  1:1332518/1‑140 (MQ=255)                                                                                            cccc‑TGGTCGCGCGGCAGGTTATGAATTTTCTGTTCAGGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                            <  1:873376/140‑1 (MQ=255)                                                                                            cccc‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTccctg                                            >  1:840334/1‑138 (MQ=255)                                                                                            cccc‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTccctg                                            >  1:290014/1‑138 (MQ=255)                                                                                            cccc‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                            >  2:661320/1‑140 (MQ=255)                                                                                            cccc‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                            >  2:1565237/1‑140 (MQ=255)                                                                                                       cgcgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAg                                  >  2:659277/1‑140 (MQ=255)                                                                                                       cgcgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAg                                  >  2:623315/1‑140 (MQ=255)                                                                                                       cgcgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAg                                  >  2:184553/1‑140 (MQ=255)                                                                                                            gagtttATGAATTTTTTGTTAATG‑AGGGAAAACCCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                             <  2:1455653/136‑1 (MQ=255)                                                                                                            cAGGTTATAAATTTTCTTTCCAGGCAGGGAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                             <  1:828574/140‑1 (MQ=255)                                                                                                            aggtttATAAATTTTCTGTTCAGGCAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                             <  1:591269/136‑1 (MQ=255)                                                                                                             agtttATGAATTTTCTGTTCATGCGGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATATAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCaa                            <  2:570671/137‑1 (MQ=255)                                                                                                             aGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCTGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCaa                            <  1:1362781/140‑1 (MQ=255)                                                                                                                         ttCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCGCACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGa                >  2:256501/1‑140 (MQ=255)                                                                                                                         ttCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGa                >  1:305337/1‑140 (MQ=255)                                                                                                                          tCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGAt               >  1:658222/1‑140 (MQ=255)                                                                                                                           ttGTTCAGGAAGGAAAAA‑CCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATg              <  2:305337/139‑1 (MQ=255)                                                                                                                              ttCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAAcctgtctc           >  1:1176803/1‑133 (MQ=255)                                                                                                                              ttCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAAcctgtctc           >  1:759084/1‑133 (MQ=255)                                                                                                                              ttCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa           >  1:1440655/1‑140 (MQ=255)                                                                                                                              ttCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa           >  2:1009333/1‑140 (MQ=255)                                                                                                                              ttCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa           >  1:671251/1‑140 (MQ=255)                                                                                                                              ttCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATCTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa           >  1:1359120/1‑140 (MQ=255)                                                                                                                                   gCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGc      >  1:670116/1‑140 (MQ=255)                                                                                                                                      gggAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCgag   >  2:1374551/1‑140 (MQ=255)                                                                                                                                       gaaaaa‑cCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCgaga  <  2:1440655/138‑1 (MQ=255)                                                                                                                                              |                                                                                                                                      CCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCC‑TGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAA‑ACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGA  >  NC_000913/3556066‑3556338

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑