Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,163	0	C	T	41.7%	61.3 / 23.3	48	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base C (5/23);  new base T (20/0);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 3.28e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCG  >  NC_000913/1487021‑1487309                                                                                                                                               |                                                                                                                                                         attaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTc                                                                                                                                                  <  1:334786/151‑1 (MQ=255)   taATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCa                                                                                                                                                 <  1:557309/150‑1 (MQ=255)        cTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAGGAAAAAAGATTTTCTCCTTTTTGAGTg                                                                                                                                            >  1:322877/1‑150 (MQ=255)         tAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAAATTTTCTCCTTTTaga                                                                                                                                               >  1:885551/1‑146 (MQ=255)            aaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCg                                                                                                                                       <  2:341625/151‑1 (MQ=255)             aCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGc                                                                                                                                      <  1:882699/151‑1 (MQ=255)             aCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAATAAGATTTTCTTCTTTTAGAGTGTTCCGc                                                                                                                                      >  2:275235/1‑151 (MQ=255)               ggTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATAAGAATTTCTCCTTTTAGAGGGGTCCGc                                                                                                                                      >  1:384837/1‑149 (MQ=255)                gTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAATAAGATTTTCTCCtttttcagtg                                                                                                                                            >  2:422211/1‑135 (MQ=255)                          aaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAGAATTTCTTCTTTTTGAGTGGTCCGCCTCTCCAta‑tt                                                                                                                          >  2:546542/1‑149 (MQ=255)                          aaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGCTTTAGAGACAAGATTTTATCCTTTCCGTATGCTCCTCtttctactcttat                                                                                                                         >  2:883261/1‑140 (MQ=255)                              tCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTAtctc                                                                                                                     <  2:360553/150‑1 (MQ=255)                              tCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGACATTTCATTTCTTCCTTTCTGAGTGCTCCGCTTCTCGCTC‑TTTtct                                                                                                                      >  2:143578/1‑149 (MQ=255)                               cAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCa                                                                                                                    <  2:409658/150‑1 (MQ=255)                                   aaTTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑g                                                                                                              <  2:678147/151‑1 (MQ=255)                                    aTTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGAAAACACAATTTTTCCCTTTCTAAATGCGCCCCCTCTCTCTT‑TTAtatccacca                                                                                                                >  2:40595/1‑144 (MQ=255)                                         gAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑t                                                                                                     <  1:515552/151‑1 (MQ=255)                                                  aaTTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAAAAAGATTTTTTCCTTTCAGAGTGCTCCGCGTCTCACTA‑TTATCTCACCCA‑GA‑A‑TTT‑TTTAgggg                                                                                              >  1:785808/1‑148 (MQ=255)                                                        ctgctgCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAACAATTTTCTCCTTTTTGAGTGCTCCGCCTCTCCCTA‑TTATTTTCCGCC‑GT‑ATTTT‑TTAAGGGAA‑GATaa                                                                                       >  1:331049/1‑150 (MQ=255)                                                          gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAagga                                                                                    <  2:575967/151‑1 (MQ=255)                                                             gcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAACGAATTTCTTCTTTTTGAGTGGTCCGCCTCTCCCTA‑TTTTTTCACCCA‑GTAA‑TTT‑TTAAGGGAAGGA‑Aagga‑gg                                                                                 >  2:383327/1‑150 (MQ=255)                                                               aaGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAAGATTTTCTCCTTTTTCAGGGCTCCCCCTTTCACTC‑TTTTTTCCCCCC‑GT‑A‑TTT‑TTAAAGGGACGATAAAGA‑GGaa                                                                               >  1:529566/1‑150 (MQ=255)                                                                 gATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAAAATTTTCTCCCTTCTGAGTGGTCCCCTTCTCCCTA‑TTATTTCACCCC‑GG‑A‑TTT‑TTTAGGGGAAGAAAaaga‑ggga                                                                               >  1:896061/1‑146 (MQ=255)                                                                    gAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATg                                                                          <  1:332581/150‑1 (MQ=255)                                                                              tATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAATACATACAAATTTTTTCTTTTTCAGTGCTCCGCTTCTCACTA‑TTATCTCACCCC‑GT‑A‑TTCTTTAAGGGAA‑GAAAAGGA‑GGAAACATGAAAATTAcccc                                                               >  2:100266/1‑151 (MQ=255)                                                                               aTCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAATAACAATTTCTCCTTTTCGGGGGCTCCCCCTCTCCCTATTTTTTTCCCCCG‑GA‑T‑TTT‑TTAAGGGAAGGAAAAGAG‑GGAACAATAAAAATTAcccc                                                               >  1:841870/1‑151 (MQ=255)                                                                                   aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGATAAAGACATAAGAATTTCTCCTTTTAGTGTGCTCCGCCTCTCACTA‑TTATCTCTCCCA‑GT‑A‑TTC‑TTAAAAGAAAGATAAGGA‑GGAAACACGaaaaataaaccgctt                                                           >  2:756604/1‑137 (MQ=255)                                                                                         tttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACATACGAATTTCTCCTTTTAGAGGGCTCCGCCCCTCACTT‑TTTTTTCACCCC‑GT‑ACTTT‑TTAAGGGAA‑GAGAAAGA‑GGAAACAAAAAAACTAACCCCCTTCCGa                                                       >  2:259414/1‑148 (MQ=255)                                                                                         tttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGTAAAAAAAAAATATTTTCTCCTTTTTGAGTGGGCCCCTTCCCCCAA‑TTTTTTCCATCA‑CG‑C‑TTT‑TTATGGGGAAGATAAAGAGGGAACCA‑GAAAAATACCCCGCTTTCGAcac                                                    >  1:915500/1‑149 (MQ=255)                                                                                          ttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGCAAGGACAAAACAATTTCTCCCTTTAGCTGGGCCCGCCTCTCCCTA‑ATATTTCACTAA‑GT‑A‑TTCTTTAAGGGAAGCATAA‑GA‑GGGACCAAGAAAATTACACCCCTTcctcccc                                                    >  2:9955/1‑145 (MQ=255)                                                                                            ccTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAAAACAAATTTCTCCTTTTAGAGTGGTCCCCCTTTCCCCC‑TTTTTTCTCGCACGA‑T‑TTT‑TTATGGGAAGGAAAAGAG‑GGAACAAGAAAAATAACCCCCTTTCCG‑CGCtt                                                  >  2:630311/1‑150 (MQ=255)                                                                                                     atatGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCaa                                        <  1:893661/151‑1 (MQ=255)                                                                                                         gTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACtat                                    <  2:561000/151‑1 (MQ=255)                                                                                                           cAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACtata                                   <  1:269374/150‑1 (MQ=255)                                                                                                                  gCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCAt                           <  2:418202/151‑1 (MQ=255)                                                                                                                    ggAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAGCGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATaa                         <  1:528348/151‑1 (MQ=255)                                                                                                                    ggAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATaa                         <  1:893172/151‑1 (MQ=255)                                                                                                                          gCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCTGACGCTTTCGCCGGCAACTATAGATGCCATAAATGtt                    >  2:37006/1‑150 (MQ=255)                                                                                                                           cGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTAt                  <  1:771390/151‑1 (MQ=255)                                                                                                                            ggTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATc                 <  1:755198/151‑1 (MQ=255)                                                                                                                               tAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCgg               <  1:780954/150‑1 (MQ=255)                                                                                                                               tAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCgg               <  2:362575/150‑1 (MQ=255)                                                                                                                               tAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCgg               >  2:781044/1‑150 (MQ=255)                                                                                                                                aaGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGa              <  2:800431/150‑1 (MQ=255)                                                                                                                                     cATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtgg        <  1:385175/151‑1 (MQ=255)                                                                                                                                     cATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtgg        >  2:179956/1‑151 (MQ=255)                                                                                                                                        aCGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtggctg     >  1:486698/1‑151 (MQ=255)                                                                                                                                            tttCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGgcg  <  1:513657/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                         ATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCA‑GT‑A‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCG  >  NC_000913/1487021‑1487309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑