Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,133,857	0	A	G	43.2%	59.0 / 10.2	45	Q19R (CAG→CGG)	flgF	flagellar component of cell‑proximal portion of basal‑body rod
Reads supporting (aligned to +/- strand):  ref base A (22/3);  new base G (0/19);  total (22/23)
Fisher's exact test for biased strand distribution p-value = 2.19e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTATCAGTCTAACGCCCAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCGGGCGCAGATATGACGCCCG  >  NC_000913/1133713‑1134006                                                                                                                                                   |                                                                                                                                                      cTATCAGTCTAACGCCCAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGt                                                                                                                                                 >  2:770557/1‑151 (MQ=255)      aGTCTAACGCCCAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCg                                                                                                                                            >  2:163624/1‑151 (MQ=255)       gTCTAACGCCCAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGc                                                                                                                                           >  2:456134/1‑151 (MQ=255)           aaCGCCCAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGcc                                                                                                                                          <  2:114250/148‑1 (MQ=255)               cccAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATc                                                                                                                                   >  1:510285/1‑151 (MQ=255)                    aCCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCCGGcc                                                                                                                              >  2:225417/1‑151 (MQ=255)                     ccAACAAACCCCAGGCCCAGACCCCCACCCCGTTGTTTAC‑CTTCCCCTAAACGCGGACGGAATACCACAAGGGATCCCGCATTTTACCCCGGGAGGGGACCCCCCAGCAAGACACTGAAACA‑ACGGGCGGTAACCGCCAGTAATCTGGCCa                                                                                                                             <  1:185580/151‑1 (MQ=255)                         cAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGc                                                                                                                         >  1:301292/1‑151 (MQ=255)                              cccAGGCCCAACCCCTAAACCCGCTGGTTAC‑CTTCCGCTAATCGCTGAGGGGATAGCTAAATGGACCACGCATTTTATCCCGCGGGGGGAGCAGCCAGCCAAACACTAAACCA‑ACGGGCGTTAACCGCCAGTAATCTGGCCAATGCCTc                                                                                                                      <  2:238410/149‑1 (MQ=255)                                  ggccaaaacccTCAACCCGCTGTTTAA‑CTTCCGCTAACCGCTGAGGGAATAGCTAAATGGACCACGCAATTTATCCCGCGAGGGGAGCACCCAGCCAGCCCCTAAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGcc                                                                                                                <  2:106032/142‑1 (MQ=255)                                  ggACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGcc                                                                                                                >  1:148379/1‑151 (MQ=255)                                    aCCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCg                                                                                                              >  2:264425/1‑151 (MQ=255)                                           ccTCACCCCGCTGTTTAA‑CTTACGCTAAGCGCTGAGGGGATAGCTAAATGGACCCCGAAATTTATCCCGCGAGGGGAGCACCCAGCCAACCCCTGAATCA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTc                                                                                                        <  2:712669/150‑1 (MQ=255)                                           ccTCACCAC‑CTGGGTAACCTTACCCTAATCGCGGACGGAATACCAAAATGAATCACGAAATTTATCCCGCGAGGGGAGCGGCCACCCAAACCCGAAATAA‑AGGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGtttt                                                                                                         <  1:38271/149‑1 (MQ=255)                                           ccTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTcg                                                                                                       >  2:620077/1‑151 (MQ=255)                                           ccTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTcg                                                                                                       >  2:303051/1‑151 (MQ=255)                                                    gCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGtt                                                                                              >  1:745836/1‑151 (MQ=255)                                                       ggTTAA‑CTTACGCTAATCGCTGCGGGAATAGCTAAATGGACCACGCAATTTATCCCGGGATGGGAGCACCCAGCAAGCCACTAAATCA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAg                                                                                                <  2:334400/146‑1 (MQ=255)                                                                tACGATAACCGCGGACGGGATAGCTAAAGGGATCCCGAAATTTATCCCGGGGGGGGAGCACCCAGCAAGCCACTGAATCA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTa                                                                                    <  1:66936/150‑1 (MQ=255)                                                                 acccaacccgcgGAGGGGAAAGCTAAAGGAACCACAAAATTTATCCCGCGAGGGGAGCCGCCAGCCAGACACTGAACCA‑ACGGGGGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCttt                                                                                     <  1:595088/140‑1 (MQ=255)                                                                 aCGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTAcg                                                                                  >  1:58293/1‑151 (MQ=255)                                                                        tCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTg                                                                           >  2:143694/1‑151 (MQ=255)                                                                         cGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGc                                                                          >  2:104017/1‑151 (MQ=255)                                                                               ggggATACCTAAATGAACCACGAAATTTATCCCGCGAGGGGAGCACCCGGCCAGCCACTGAATCA‑ACGGGGGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTgg                                                                    <  1:622421/150‑1 (MQ=255)                                                                                ggaaTAGCAAAAGGGACCCCGAAATTTACCCCGCGAGGGGGGCACCCAGCCAGACACTAAAACA‑CCGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTg                                                                     <  2:35722/146‑1 (MQ=255)                                                                                 gtttgcccgaaTGGAGCACCAATTTTATACCTCGGGGGAATCACCAAGCCAGACATTAATTCA‑CCGGTTGTAAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGaa                                                                  <  2:257027/142‑1 (MQ=255)                                                                                    tAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAggg                                                               >  1:468161/1‑151 (MQ=255)                                                                                        tCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCttt                                                           >  2:505922/1‑151 (MQ=255)                                                                                        acAATGGACCCCGCAATTTAACCCGCGATGGGAGCACCCACCTAGACCCTGAACCA‑ACGGGCGGAACCCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCttt                                                           <  2:579123/150‑1 (MQ=255)                                                                                          aagggATCACTAATTTTATCCCGCGATGGGAGCACCCACCCAGACACTAAATAA‑ACGGGCGGAAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCttt                                                           <  2:492131/146‑1 (MQ=255)                                                                                                   cGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTAAGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCAcg                                                >  2:416310/1‑151 (MQ=255)                                                                                                      attttaccccGCGAGGGGAGCCGCCAGCCAGCCACTAAAACA‑ACAGGGGCTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACgcgc                                             <  1:319700/143‑1 (MQ=255)                                                                                                      aaTTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACgcgc                                             >  2:29736/1‑151 (MQ=255)                                                                                                          tataCCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGt                                         >  1:530479/1‑151 (MQ=255)                                                                                                              ccGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGt                                     >  2:541592/1‑151 (MQ=255)                                                                                                                     gggAGCAGCCAGCCAACCCCGAAATCA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTc                                    <  2:181680/145‑1 (MQ=255)                                                                                                                     gggAGCAGCCAGCAAGACAC‑CAATAACCCTGGTGGAAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTgg                                      <  1:696442/143‑1 (MQ=255)                                                                                                                       gAGCAGCCAGCCAGACACTAAATCA‑ACGGGCGTTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTc                            <  2:332601/151‑1 (MQ=255)                                                                                                                       gAGCAGCCAGCCAGACACTAAATAA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTc                            <  2:58094/151‑1 (MQ=255)                                                                                                                            cccagccacACCCGAAACCA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGc                       <  2:42866/150‑1 (MQ=255)                                                                                                                              cagcgagCCACTAAACCA‑ACGGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCg                     <  2:4517/151‑1 (MQ=255)                                                                                                                                cccagACCCTAAAACA‑CCGGGCGTAAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCg                     <  1:358673/148‑1 (MQ=255)                                                                                                                                  cagACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCGGgcg                 >  1:774890/1‑151 (MQ=255)                                                                                                                                   agACACTAAAAAA‑AGGGGGGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCa                           <  2:366054/140‑1 (MQ=255)                                                                                                                                             tCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCGGGCGCAGATATGACg      >  2:252972/1‑151 (MQ=255)                                                                                                                                                   aGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCGGGCGCAGATATGACGCCCg  >  1:415150/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                      CTATCAGTCTAACGCCCAGACCATCAAAACCCAGGACCAGATCCTCAACACGCTGGTTAA‑CTTACGCTAATCGCTGACGGGATAGCTCAATGGATCACGCAATTTATACCGCGATGGGAGCAGCCAGCCAGACACTGAATCA‑ACAGGCGGTAACCGCCAGTAATCTGGCCAATGCCTCAACGCCCGGTTTTCGCGCGCAGTTGAATGCTTTACGCGCGGTGCCAGTGGAAGGGCTTTCTCTGCCCACGCGCACGTTGGTCACGGCGTCAACGCCGGGCGCAGATATGACGCCCG  >  NC_000913/1133713‑1134006

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑