Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	650,464	0	A	T	48.7%	22.8 / 25.1	40	R9R (CGT→CGA)	citE	citrate lyase, citryl‑ACP lyase (beta) subunit
Reads supporting (aligned to +/- strand):  ref base A (4/16);  new base T (19/0);  total (23/17)
Fisher's exact test for biased strand distribution p-value = 1.54e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGTCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATTCAGCTGTACGC  >  NC_000913/650330‑650605                                                                                                                                        |                                                                                                                                                  gtgtCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGG‑GGGTTTTTC‑GTTGTTGCAGccgaa                                                                                                                                  >  1:642387/1‑147 (MQ=255)   gtCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGG‑GGGGTTTTC‑GTTGTTGCAGC‑GAAGCg                                                                                                                               >  2:256204/1‑151 (MQ=255)       ttttCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGG‑GGGGTTTTC‑GTTTTTGCCGC‑GAAACGG‑aaa                                                                                                                          >  2:107588/1‑151 (MQ=255)       ttttCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGCGGGGTTTTTG‑GTTGTTGcgaggagcgggaa                                                                                                                             >  2:110157/1‑139 (MQ=255)       ttttCACGCAATGCTACGGAGTCGTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑aaa                                                                                                                          <  2:69169/151‑1 (MQ=255)         ttCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATc                                                                                                                        <  1:84917/151‑1 (MQ=255)               cAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGG‑GAGGTTTTA‑GTTTTTTCAGC‑GAAGCGG‑AGATCA‑TTgg                                                                                                                  >  1:222761/1‑150 (MQ=255)               cAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGc                                                                                                                 <  2:487465/151‑1 (MQ=255)               cAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGC‑GGGTTTTTCTTTTTTTGCGGC‑GATCCGG‑aaaacttgg                                                                                                                    >  2:591786/1‑144 (MQ=255)                 aTGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GGGTGTTTT‑GTTGTTGCAGC‑GAAAAGG‑GAATCA‑ATGGCaa                                                                                                               >  1:376341/1‑151 (MQ=255)                 aTGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GGGGTTTTT‑GTTGTTGCAGC‑GAAACGG‑GAAACA‑TTTGCaa                                                                                                               >  2:46043/1‑151 (MQ=255)                 aTGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GGGGTTTTC‑GTTTTTTCCGC‑CCAACGG‑GAATCC‑TTTGCaa                                                                                                               >  2:150148/1‑151 (MQ=255)                 aTGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GGGGTTTAC‑GTTGTTGCAAG‑GAAGCGG‑AAAACA‑TTGGCaa                                                                                                               >  2:290736/1‑151 (MQ=255)                             cTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GGGGTTTTC‑GTTGTTTCCGG‑GAAACGG‑AAAACA‑ATGGCAATCCTCCCCTggg                                                                                                   >  2:42775/1‑150 (MQ=255)                             cTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGc                                                                                                   <  1:649863/151‑1 (MQ=255)                             cTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGc                                                                                                   <  1:571478/151‑1 (MQ=255)                             cTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGc                                                                                                   <  2:332995/151‑1 (MQ=255)                                        aaCATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGAt                                                                                        <  1:252197/151‑1 (MQ=255)                                          cATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGG‑GGGGTTTAC‑GGTTTTGCCGCGGAAGGGG‑AAA‑CA‑TTGGGAAACCCCCCCTGGCAGGACCGGGGTa                                                                                       >  2:502498/1‑150 (MQ=255)                                               gggCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGC‑GGGGTTTTC‑CTTGTTTGAGC‑GAAGAGG‑GAAACA‑TTGGGGATCCTCCCCTGTGAGAGACCGGATAcccccg                                                                                 >  1:559293/1‑147 (MQ=255)                                                 gCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGG‑GGGGTTTTC‑GTTTTTGCCGC‑GAAGCGG‑AAAACATTTGGCAA‑CCTCCCCCGGCAGGGCCGGGGTAcccccggg                                                                               >  2:121063/1‑145 (MQ=255)                                                              aGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGG‑GGGGTTTTA‑GGTGTTTGAGC‑GAAGAGG‑GAAACA‑ATTGGAAACCTCCCCTGGCAGAGCCGGGGGACCGCCGGCGCGGGCCCGCCgg                                                                  >  2:18310/1‑151 (MQ=255)                                                               gATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGG‑GGGGTTTTC‑GTTTTTGCCAC‑GAAACGG‑AAAACA‑ATGGCAAACCCCCCCCGGCAGGGGCCGGGTACCCCCGGCGCGGGCCCGCCggg                                                                 >  2:519196/1‑151 (MQ=255)                                                               gATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGC‑GGGATTTTC‑GTTGTTGCACG‑GAAAAGGAAAAAAA‑ATGGCAATCC‑CCCATGGGGGGGCCGGGGTACCCCCGGcgcgggggcggaagg                                                                 >  2:316715/1‑140 (MQ=255)                                                                         ttGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGG‑GGGGTTTTT‑CTTTTTGGACC‑GAAACGG‑GAATCA‑TTTGGAAAACCCCCCCGTCCGAGCCGGGGTACCGCCGGCGCGTGGCAGCACGGCTTccccccg                                                       >  1:502747/1‑146 (MQ=255)                                                                         ttGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGt                                                         <  2:497764/149‑1 (MQ=255)                                                                         ttGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGt                                                         <  2:249213/149‑1 (MQ=255)                                                                         ttGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGt                                                         <  2:165135/149‑1 (MQ=255)                                                                                        gCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGc                                         <  1:547581/150‑1 (MQ=255)                                                                                        gCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGC‑GGGTTTTTT‑GTTTGTTCCGC‑GAAGCGG‑CAAACA‑TTGGCCAACCTCCCCTGGCAGGGACGGGGGAACGCCGGCCCGGGCCCGCCGGGCGTCCCCTCGGTGACGTCAAATGCa                                        >  2:349089/1‑151 (MQ=255)                                                                                        gCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGGGC‑GGGGTTTAT‑GGTTTTGCCGC‑GAAGAGG‑AAAACC‑TTGGCAATCCCCCCATTGCAGAGCCGGGGTACCGCCGGCGCGTGGCAGCCGGGGTTCCCGTCGTGCACGTcaaaaaca                                        >  1:440274/1‑147 (MQ=255)                                                                                          aTTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGt                                      <  2:472160/151‑1 (MQ=255)                                                                                            tGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTcc                                    <  1:53185/151‑1 (MQ=255)                                                                                                    ggCACAAACAACATGCTGCGGCGGGTGC‑GGGGTTTAC‑GGTTTTGCCGC‑GAAAGGG‑AAAAAA‑ATGGCAATCCCCCCCTGGGGGAGGCGGGGGACCGCTGGGGCGGGCCAGCAGGGGTTCCAGTCGTTGCCGTAAAAAGCAGGcccgggggc                             >  2:594858/1‑143 (MQ=255)                                                                                                    ggCACAAACAACATGCTGCGGCGGGTGC‑GAGGTTTTA‑GTTGTTGCAGG‑GAAACGG‑GAAACA‑TTGGCAAACCCCCCATTGGAGAGCCGGGGAACCCCCGGCGCGGGCCCCCAGGGGGTCCCGTCCGGCACGGAAAAAGCCGGCCCGGgcgc                             >  2:518617/1‑150 (MQ=255)                                                                                                        caaacaaCATGCTGCGGCGGGGGC‑GAGTTTTTC‑GTTTTTTCAGC‑GAAACGG‑AAAAAA‑TTGGGAAACCTCCCATGGCCGAAGCGGGGTACCGCTGGCGCGTGCCCGCAGGGCCTTCCGTCGTGCCCCTTAAATTCCGTCCCGTGCGCCcttt                        >  1:61783/1‑150 (MQ=255)                                                                                                                        gcggGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATTCAGc         <  1:150110/150‑1 (MQ=255)                                                                                                                           ggTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATTCAGCTGt      <  2:126697/150‑1 (MQ=255)                                                                                                                             tGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATTCAGCTGTAc    <  1:110135/150‑1 (MQ=255)                                                                                                                               c‑GAGTTTTGC‑GTGGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAAGCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTTCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATTCAGCTGTAcgc  <  2:266627/150‑1 (MQ=255)                                                                                                                                        |                                                                                                                                                  GTGTCTTTTTCACGCAATGCTACGGAGTCTTCGAGGTCAAACATCAGGGCATCAGCCGGGTAGATGAAGGAGTTGCTGACCATCGCGGCATTGGCACCAGGCACAAACAACATGCTGCGGCGGGTGC‑GAGTTTTAC‑GTTGTTGCAGC‑GAAGCGG‑AAATCA‑TTGGCAATCCTCCCATGGCAGAGCCGGGATACCGCTGGCGCGTGCCAGCAGGGCTTCCAGTCGTGCACGTAAAATGCAGTCCAGTGCGCCTTTGTCATCGACATTCAGCTGTACGC  >  NC_000913/650330‑650605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑