Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,903,692	0	C	A	41.5%	85.3 / 27.6	53	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
Reads supporting (aligned to +/- strand):  ref base C (2/29);  new base A (22/0);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 5.97e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

AAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAA  >  NC_000913/2903550‑2903839                                                                                                                                               |                                                                                                                                                          aaGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑Att                                                                                                                                                  <  2:526334/151‑1 (MQ=255)              tACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAACAAAC‑ATTATACTC‑caaa                                                                                                                                       >  1:1014904/1‑148 (MQ=255)                cacTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACCC‑ATTaaaccctaaaaaaa                                                                                                                                    >  2:783209/1‑137 (MQ=255)                 acTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACAC‑ATTAGCCTC‑AAAACaaaa                                                                                                                                  >  1:492361/1‑149 (MQ=255)                   tCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACACCC‑CATATCCTC‑TAaaaaaaaa                                                                                                                                 >  2:380556/1‑147 (MQ=255)                        gTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑t                                                                                                                         <  1:791274/150‑1 (MQ=255)                            ttAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCa                                                                                                                     <  1:662935/150‑1 (MQ=255)                              aGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGa                                                                                                                   <  2:956540/150‑1 (MQ=255)                              aGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGAt                                                                                                                  <  1:850320/151‑1 (MQ=255)                                            tACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTTAAAAAAATCAATTAACC‑C‑CAAACAAAAAA‑AAAC‑CTCCCGATTTATTAAtt                                                                                                         >  1:299247/1‑146 (MQ=255)                                               gAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAAAAATC‑CTTTACCCC‑AAAACAAAAAA‑AAAA‑ATACAGATTTTTTTATTaaaaaa                                                                                                   >  1:649005/1‑145 (MQ=255)                                                 aTCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGaa                                                                                              <  2:453571/151‑1 (MQ=255)                                                     cACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAAAACAC‑AATAGACCC‑AAAAAAAAAAC‑AAAA‑TTCCAGATTTATTTATTAAAC‑AATGAAT‑aa                                                                                          >  1:117693/1‑150 (MQ=255)                                                       cTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAACACCC‑ATTAACCTC‑CAAAAAAAAAA‑AAAA‑ATTCAGATTTTTTTTTTAAAC‑AAAAAAT‑aaaa                                                                                        >  2:486586/1‑148 (MQ=255)                                                       cTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACa                                                                                        <  2:25712/150‑1 (MQ=255)                                                        tttATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAACACTC‑CTTATCCTC‑AAAACAAAAAA‑AAAA‑TTTCACATTTTTTACTTTAAC‑aaaaaaaaaaaa                                                                                        >  2:745518/1‑140 (MQ=255)                                                          tATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTTAAAACACTC‑ATTAACCTC‑AAAACAAAAAC‑AAAC‑TTCCTGATTTATTAATTAATC‑AAAGAAT‑Aaaaa                                                                                       >  1:553652/1‑148 (MQ=255)                                                           aTCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCt                                                                                    <  2:344472/150‑1 (MQ=255)                                                           aTCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACCCCC‑CTTTGCCTC‑AAAAAAAAAAA‑AAAA‑TTCCAGAATTATTTTTTTACC‑AAAAAAA‑AACAAACtt                                                                                   >  2:431344/1‑151 (MQ=255)                                                                 tttCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTaaaaa                                                                              <  2:752245/150‑1 (MQ=255)                                                                         aaaGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTC‑ATTAGCCTC‑AAAAAAAAAAA‑AAAC‑ATCCAGATTTTTTTTTTAACC‑AAAGAAT‑AAAAAACTTAAAAAata                                                                           >  2:559017/1‑145 (MQ=255)                                                                         aaaGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGt                                                                     <  1:896803/151‑1 (MQ=255)                                                                          aaGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGCTTTTTTAAAAAAAAC‑AATTGCCTC‑AAAAAAAAAAA‑AAACATTCCA‑ATTTATTATTTAAAC‑AAAAAAT‑AAAAAAAATAAAAAAAAAAATGtt                                                                    >  1:512948/1‑151 (MQ=255)                                                                            gTATGAACTGGATATTTTTAGTCATAAGAACTATTCAACAACAGCGTATAGACGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATGTCCTGTTa                                                                   <  1:859191/150‑1 (MQ=255)                                                                            gTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTAt                                                                  <  1:92630/151‑1 (MQ=255)                                                                              aTGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAAAAATC‑CTTATCCTC‑AAAAAAAAAAA‑AAAA‑CTTCACATTTAATATTTAAAC‑AAAAAAA‑AAAAAACTTAAAAAAAAAAATGTtttt                                                                 >  1:446882/1‑150 (MQ=255)                                                                              aTGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGGTTTCTTAAAACACGC‑CATTGATAC‑AAAAAAAAAAA‑AAAC‑ATCCAGATTTATTTTTTTACCAAATTAAT‑AAAAACTTTaaaaaaaaacagtt                                                                     >  1:479251/1‑139 (MQ=255)                                                                                gAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAACACTC‑CTTAGCCTC‑CAAAAAAAAAA‑AAAA‑ATCCAGATTTTTTTCTTTACC‑AAAAAAA‑AAAAAACTTAAAAAAAATAATGTtttttt                                                               >  2:407996/1‑148 (MQ=255)                                                                                     ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGaa                                                         <  2:377868/151‑1 (MQ=255)                                                                                        tatCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAAAACCC‑ATTCACCTCAAAAAAAAAAAA‑AAAC‑TTCCGCATTATTTATTAAACC‑AACAAAA‑AAAAAAC‑TAAAAAAAATTATGTTTTTTTaaaaaaaa                                                       >  2:555907/1‑150 (MQ=255)                                                                                         atCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAAAAATC‑AATTTACTC‑AAAACAAAAAC‑AAAA‑ATCCAGATTTATTATTTAAAC‑AATGAAT‑AAAAAACTTAAAAAATATACTATTATTTTAAAGaaaaa                                                      >  1:829269/1‑150 (MQ=255)                                                                                            tttATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAAAACAC‑ATTAGACTC‑AAAACAAAAAC‑AAAC‑TTCCAGATTTATTTCTTAAAC‑AAATAAA‑AAAAAACTTAAAAAAAATAATTTTATTTTTAATaaaaaa                                                     >  1:422522/1‑148 (MQ=255)                                                                                             ttATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAAt                                                    <  2:525842/148‑1 (MQ=255)                                                                                                 tCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAg                                              <  1:994485/150‑1 (MQ=255)                                                                                                 tCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAg                                              <  2:438979/150‑1 (MQ=255)                                                                                                 tCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAg                                              <  1:27242/150‑1 (MQ=255)                                                                                                  cATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTATTAAACCCCCC‑AATAACCTC‑CAAACAAAAAA‑AAAA‑TTCCCGATTTTTTAATTTACC‑AATTAAA‑AAAAAAATTTAAAAAAATAATGTTTTTCTTAAAAAAAAATTaaaaag                                             >  2:757825/1‑146 (MQ=255)                                                                                                      aGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTa                                        <  2:46455/151‑1 (MQ=255)                                                                                                       gAACTATTCATCAACAGCGTATAGAGGCGGTTGTTTGAAAAAACAC‑AATTAACTC‑AAAAAAAAAAA‑AAAC‑TTTCAGATTTTATACTTAAAC‑AAAGAAA‑AAAAAAAAAAAAAAAAATAAAATTATTTTTAaaaaaaaaaaaaaa                                               >  1:37406/1‑137 (MQ=255)                                                                                                        aaCTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAAt                                      <  2:776800/151‑1 (MQ=255)                                                                                                         aCTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATCCTGTTATTCTAAAGAAAAAATTAACAGGCATTAAtt                                     <  1:695931/151‑1 (MQ=255)                                                                                                            aTTCATCAACAGCGTATAGAGGCGGGTATGTTAAAACAACC‑ATTTTCCCC‑AAAACAAAAACAAAAA‑TTCCGGATTT‑TTTCTTTACC‑AAATAATAAAAAAACTTAAAAAAAAAATTTTTTTTTTAAAAAAAAAATAAAAAGG‑ATTaa                                       >  1:62186/1‑146 (MQ=255)                                                                                                             ttCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCaa                                  <  1:538614/150‑1 (MQ=255)                                                                                                              tcatcaACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAat                                 <  2:167155/150‑1 (MQ=255)                                                                                                               catcaACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAata                                <  2:71461/150‑1 (MQ=255)                                                                                                                  caACAGCGTATAGAGGCGGTTATTTAAAAACCCTC‑ATTTACCCC‑AAAAAAAAAAA‑AAAC‑CTCCAGAATTTTTTTTTAACC‑CAAAAAA‑AAAAAAAATAAAAAAAAAAATTTTTTTTTTAAAAAAAAAATAACAAACAATAAATTAATAtt                              >  1:263275/1‑149 (MQ=255)                                                                                                                           ataGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAaataat                   <  1:886787/151‑1 (MQ=255)                                                                                                                           ataGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTA‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAaataa                    <  1:528797/150‑1 (MQ=255)                                                                                                                                  cGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTa             >  1:690104/1‑150 (MQ=255)                                                                                                                                   ggTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTaaa           <  1:559013/151‑1 (MQ=255)                                                                                                                                    gTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTaaaa          <  2:447115/151‑1 (MQ=255)                                                                                                                                       aTGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAAtt        <  1:214794/150‑1 (MQ=255)                                                                                                                                            aaaCCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTaa  <  2:705173/151‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                          AAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTC‑ATTAGCCTC‑AAAACAAAGAC‑AAAC‑TTCCAGATTTATTACTTAACC‑AATGAAT‑AACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAA  >  NC_000913/2903550‑2903839

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑