Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,958,771	0	A	T	48.6%	41.3 / 15.8	35	D38E (GAT→GAA)	ptrA	protease III
Reads supporting (aligned to +/- strand):  ref base A (1/17);  new base T (16/1);  total (17/18)
Fisher's exact test for biased strand distribution p-value = 7.16e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCCTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAAT  >  NC_000913/2958630‑2958900                                                                                                                                               |                                                                                                                                         ccccTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTCACttttt                                                                                                                                 >  2:75479/1‑150 (MQ=255)    cTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACgg                                                                                                                              <  2:2825/151‑1 (MQ=255)      ggTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTACtttttccggt                                                                                                                            >  2:233459/1‑145 (MQ=255)      ggTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTACTTTTTAGGAt                                                                                                                            >  2:3634/1‑151 (MQ=255)            ccTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTTACCTTTTCGGGTGGgttt                                                                                                                      >  2:87792/1‑150 (MQ=255)            ccTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTCACttttttgggtgggttt                                                                                                                      >  1:219368/1‑139 (MQ=255)             cTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTcc                                                                                                                     <  2:245362/151‑1 (MQ=255)               cGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTg                                                                                                                   <  2:551313/151‑1 (MQ=255)                              aCCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATcc                                                                                                   <  2:472367/151‑1 (MQ=255)                                ccAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCg                                                                                                 <  2:269733/151‑1 (MQ=255)                                    cGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTc                                                                                             <  2:344899/151‑1 (MQ=255)                                                          cGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGGTTTATTTTTTTCATTTTTAGGATTGTTTTTCTAAAT‑CGCCGGCC‑TCCCCTTTTTGTCT‑TGAA‑TT‑AAGGGGGccaa                                                                    >  1:283211/1‑149 (MQ=255)                                                           gATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACgg                                                                                                                              <  2:149142/96‑1 (MQ=255)                                                            aTTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTACTTTTACGGATGGGTTTCTTAAT‑CGGCTGCCCTCCCGTTTCTT‑CC‑TTAC‑TTAAAGGGTGCCaaaa                                                                  >  2:13236/1‑151 (MQ=255)                                                             tttAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAgg                                                                <  1:327049/151‑1 (MQ=255)                                                                  ctgcctgcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAAc                                                           <  2:1587/151‑1 (MQ=255)                                                                    gcctgcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGTGG‑TTTTCTTTTTTACTTTTTCGGGTGGGTTTCTTAAT‑CGGCTGCCCTCCCCTTTCTT‑CC‑TGGCTTT‑AAGGGGCCCCAAAGGG‑AACTa                                                         >  2:183618/1‑151 (MQ=255)                                                                      ctgcGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATAGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTaa‑c                                                      <  2:196033/151‑1 (MQ=255)                                                                                     cAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑GTCTACTTTTTACCTTTTTGGTACGTTTTTTGCAT‑CCGCCGCCCTCACCCTTCTT‑CC‑TCAC‑CT‑CAGGGCGCCCAAAAGGCCACAAATCAA‑Aaataaactctt                                       >  1:509907/1‑145 (MQ=255)                                                                                            accaccATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAgg                               <  2:244730/151‑1 (MQ=255)                                                                                             ccaccaTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTCTTTTTTTCACTTTTTTGGATGGGTTTCTGTATATGGGTGCCCCCCGTTTTTTT‑CT‑TGCT‑TT‑AAGGGGGCCCAAAAGG‑GACTAA‑AAA‑CAATAAATCTTTTAAACaagg                              >  1:324946/1‑148 (MQ=255)                                                                                             ccaccaTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTTTCACTTTTACGGATGGTTTTCTGAAT‑CCGCTGCCATCCCCTTTTTT‑CC‑TGAC‑TT‑AAGGGGGGCCAAAGGGGAACTAA‑AAA‑Caaaaaatattttaaaccggg                              >  2:302988/1‑136 (MQ=255)                                                                                             ccaccaTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGt                              <  1:421899/151‑1 (MQ=255)                                                                                               accaTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTTTTTTTTACTTTTTCCGGTGGTTTTCCGTAT‑CGGCTGCCATCCCCCCTTTG‑GC‑TTAC‑CT‑TAGGGGGCCCCAAAGGGAACAAA‑AAA‑AAACAAATCTTTTAACCAggggt                            >  2:86833/1‑148 (MQ=255)                                                                                                  aTACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTTTCTTTATTACTTTTACCGAATGTTTTCTGAAA‑CAGCCTCCCACCCCTTTCTT‑CC‑TTAA‑TT‑TAAGGTGGCCCCAAGGCAACAAA‑CAACCAAAAATACTTTGAACAAgtggtgg                          >  1:544616/1‑145 (MQ=255)                                                                                                     ccGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTACTTTTTAGGATGGGTTTCTGAAA‑CGGCTGCCCTCCCCTTTCTT‑CC‑TGAC‑TT‑TAGGGGGGCCCAAAGGCAACTAA‑AAA‑CAAAAATGCTTTTAACCAAGTGCTGCggg                      >  2:91501/1‑151 (MQ=255)                                                                                                       gTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATTTTTTTTACTTTTTTGGGTGGTTTTCTGAAT‑ATGGTGCCCTCCCGTTTTTG‑TC‑TGAC‑TT‑AAGGGGGCCCAAAAGGCAACTAA‑AAA‑AAAAAAATCTTTTAAACAAGTGGGGCggggg                    >  1:473905/1‑150 (MQ=255)                                                                                                         tATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCAt                  <  1:325470/151‑1 (MQ=255)                                                                                                                aCGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCAc              <  2:407701/148‑1 (MQ=255)                                                                                                                 cGTATAGCCTGATACTGGCGG‑TTTTTTTTTTTACTTTTTCGGATGGTTTCCTTAAT‑CTGCTGCCCTCCCCCTTTTT‑CC‑TGACTTT‑AAGGTGGCCCAAAGGG‑AAATAA‑AAA‑AAAAAAAGCTTTTTAACAGGGGCTggggggggtttccggg           >  2:144400/1‑140 (MQ=255)                                                                                                                 cGTATAGCCTGATACTGGCGG‑TTATCTTTTTATCTTTTTCTGGTGGTTTTCTGAATCCGGCGGCCA‑CCCGTTTTTT‑CCTTGCT‑TT‑TAGGCGGCGCAACGGG‑AGCTAA‑CCA‑CCATAATTATTTGCTCCCGGCGCCGCGGGGcggttctcgg           >  1:337566/1‑141 (MQ=255)                                                                                                                 cGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAggg                                                                          <  2:499185/89‑1 (MQ=255)                                                                                                                        ccTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATaa   <  2:260112/151‑1 (MQ=255)                                                                                                                         cTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAAt  <  2:409218/151‑1 (MQ=255)                                                                                                                         cTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAAt  <  1:217638/151‑1 (MQ=255)                                                                                                                                               |                                                                                                                                         CCCCTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGG‑TTATCTTTATCACTTTTACGGATGGTTTCCTGAAT‑CGGCTGCCATCCCGTTTCTG‑CC‑TGAC‑TT‑AAGGGTGCCCAAAGGGCAACTAA‑CAA‑CAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAAT  >  NC_000913/2958630‑2958900

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑