Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,958,771	0	A	T	52.2%	19.8 / 37.7	23	D38E (GAT→GAA)	ptrA	protease III
Reads supporting (aligned to +/- strand):  ref base A (1/10);  new base T (12/0);  total (13/10)
Fisher's exact test for biased strand distribution p-value = 9.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.04e-05

CCCCTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAAT  >  NC_000913/2958630‑2958909                                                                                                                                               |                                                                                                                                              ccccTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTTTTACttttt                                                                                                                                      >  1:15063/1‑150 (MQ=255) ccccTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGGTATCTTTTTTCCttttt                                                                                                                                      >  2:308261/1‑150 (MQ=255)                   aTCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGCGGGTTTTCTTTTTC‑CCTTTAAGGATggggttacgaaa                                                                                                                     >  1:271455/1‑140 (MQ=255)                   aTCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAAt                                                                                                                     <  2:96897/150‑1 (MQ=255)                                  aaCGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGtt                                                                                                    <  1:467529/151‑1 (MQ=255)                                      ggCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTTTCTCTTTTACGGATGGGTTTCTGTATT‑GGGCGCCCTCCCCtttttt                                                                                                >  2:85190/1‑148 (MQ=255)                                          ccaccaGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGGTTTCTTTTTTACTTTTTTGGGGGGGTTTTTGAATCGGGCTGCC‑TCCCCTTTTTGTC‑tt                                                                                           >  1:338456/1‑150 (MQ=255)                                           caccaGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTTTTTTTTTTACTTTTTCGGATGGGTTTCTTAAAC‑GGCTGCCATCCCCTTTTTTCC‑t                                                                                            >  2:203472/1‑149 (MQ=255)                                           caccaGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTTTTACTTTTTCGGATGGGTTTCTGAATC‑GGCTGCCATCCCCttttttc                                                                                               >  2:468728/1‑143 (MQ=255)                                            accaGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGAc                                                                                         <  2:373240/151‑1 (MQ=255)                                                   ccGAGAGCGATTTAACTTCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAggg                                                                                 <  1:208069/151‑1 (MQ=255)                                                   ccGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAggg                                                                                 <  1:20201/151‑1 (MQ=255)                                                   ccGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAggg                                                                                 <  1:39495/151‑1 (MQ=255)                                                                                             ccaccaTACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTTTCTCTTTTTTGGATGGGTTCCTTAATC‑GGCTGGCATCCCGTTTCTGCC‑TGACTT‑TAAGGTGGCCAAAAGGGAACTAACAACAAAAATACTTTTTACCAggg                                       >  2:446071/1‑150 (MQ=255)                                                                                                    aCCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTTTCACTTTTATGGAAGGGTTTCTGAAAC‑CGCCGGCCTCCCCTTTCTGCCTTGCTTT‑ATGGGGGCGCAAA‑GGCAACTAACAACAAAAAAGCTTTGCACCAgggggcgcgg                                >  1:238502/1‑143 (MQ=255)                                                                                                    aCCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCgg                                <  2:159798/151‑1 (MQ=255)                                                                                                     ccGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTTTCTTTTTTACCTTTTCGGGAGGGTTCCTTAATC‑GGCTGCCATCCCCCTTCTTCC‑TCACTT‑TAAGGGGCCCCAAAGGCAACCAAAAACAAAAATGCTTTTAACCCGGTGCTGCggg                               >  2:438083/1‑151 (MQ=255)                                                                                                     ccGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATTTTTTTTACTTTTTCGGGTGGTTTTCTTAATC‑GGCTGCCCTCCCGTTTTTTCC‑TGACTT‑AAAGGGGCCCCAAAAGCAACTAACAAAAATAAAGCTTTTTAACAAGTGCTGCggg                               >  1:400759/1‑151 (MQ=255)                                                                                                      cGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCgggg                              <  2:190572/151‑1 (MQ=255)                                                                                                          aTCCAGACGTATAGCCTGATACTGGC‑GGTTTTCTTTTTTACTTTTTCGGATGGGTTTCTGAAAT‑GGCTGCCATCCCCCTTTTTCC‑TGACTTAAAGGGGGCCCAAA‑GGCAAATAACAACAAAAATGCTTTTTACCAGGGGCTGCggggggtt                          >  2:157331/1‑147 (MQ=255)                                                                                                                   tataGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGAGGCATTCACGGAcc                  <  2:217033/150‑1 (MQ=255)                                                                                                                                 ggC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTaa   >  1:38392/1‑151 (MQ=255)                                                                                                                                   c‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAAt  <  2:101504/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                              CCCCTGGTACGCCTCGGGATCTTCCAGCGACCCAACGGGCACCACCAGCGCCGAGAGCGATTTAACTGCCTGCGGATCAGAAACCAGCAAGACCACCATACCGTTATCCAGACGTATAGCCTGATACTGGC‑GGTTATCTTTATCACTTTTACGGATGGTTTCCTGAATC‑GGCTGCCATCCCGTTTCTGCC‑TGACTT‑AAGGGTGCCCAAAGGGCAACTAACAACAATAATGCTTTGAACCAGGTGCTGCGGGGCATTCACGGACCTCATAATCAACTTAAT  >  NC_000913/2958630‑2958909

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: ‑