Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,011,426	A→C	intergenic (+13/‑35)	hyuA → / → yqeA	phenylhydantoinase/putative amino acid kinase YqeA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,011,426	0	A	C	97.6%	153.2 / ‑3.4	41	intergenic (+13/‑35)	hyuA/yqeA	phenylhydantoinase/putative amino acid kinase YqeA
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base C (22/18);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 4.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGTCAGGGCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGAT  >  NC_000913/3011288‑3011562                                                                                                                                           |                                                                                                                                         tGTCAGGGCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGAt                                                                                                                                         <  2:1094616/140‑1 (MQ=255)    cAGGGCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCta                                                                                                                                      >  1:233996/1‑140 (MQ=255)     aGGGCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCtat                                                                                                                                     <  2:958054/140‑1 (MQ=255)      gggCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCtata                                                                                                                                    <  2:58839/140‑1 (MQ=255)       ggCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATac                                                                                                                                   >  1:103024/1‑140 (MQ=255)          gcgATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGTCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATAcaca                                                                                                                                <  1:888161/140‑1 (MQ=255)          gcgATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATAcaca                                                                                                                                <  1:238915/140‑1 (MQ=255)                        cTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAAtgatga                                                                                                                  >  1:363385/1‑140 (MQ=255)                        cTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAAtgatga                                                                                                                  >  1:519341/1‑140 (MQ=255)                                 tggtgAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGaaa                                                                                                         >  1:684214/1‑140 (MQ=255)                                 tggtgAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGaaa                                                                                                         >  1:85447/1‑140 (MQ=255)                                      aaaCGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGa                                                                                                    >  1:264509/1‑140 (MQ=255)                                          gATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTaa                                                                                                <  1:991674/140‑1 (MQ=255)                                          gATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTaa                                                                                                <  2:685976/140‑1 (MQ=255)                                               tCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGaaaa                                                                                           <  2:85447/140‑1 (MQ=255)                                                cTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAAt                                                                                          <  2:393954/140‑1 (MQ=255)                                                      cGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTtct                                                                                    >  2:1279517/1‑140 (MQ=255)                                                         cACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGc                                                                                 >  2:97824/1‑140 (MQ=255)                                                          aCCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCCAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGcc                                                                                <  2:793908/140‑1 (MQ=255)                                                           ccTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGccc                                                                               <  2:1021180/140‑1 (MQ=255)                                                             tttACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTg                                                                             >  1:839520/1‑140 (MQ=255)                                                                      aaaGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAAt                                                                    >  2:571635/1‑140 (MQ=255)                                                                       aaGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGcc                                                                                <  1:1311908/127‑1 (MQ=255)                                                                       aaGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGcc                                                                                >  2:1311908/1‑127 (MQ=255)                                                                          ccGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATgcgc                                                                <  1:690460/140‑1 (MQ=255)                                                                           cGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCt                                                               <  2:1025347/140‑1 (MQ=255)                                                                           cGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCt                                                               <  2:264509/140‑1 (MQ=255)                                                                                              cGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCggg                                            >  2:818469/1‑140 (MQ=255)                                                                                                aCGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCg                                                          <  1:734798/124‑1 (MQ=255)                                                                                                aCGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCg                                                          >  2:734798/1‑124 (MQ=255)                                                                                                             gTCCCTCCCGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTa                             <  2:363385/140‑1 (MQ=255)                                                                                                               ccctcccGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTaaa                           <  1:97824/140‑1 (MQ=255)                                                                                                                  tcccGTGCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAAt                        >  1:549521/1‑140 (MQ=255)                                                                                                                    ccGTGCTCTAACCACTGCGAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCGCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAACTGAAAGCGGTAAAAATTa                      <  2:756081/140‑1 (MQ=255)                                                                                                                        gCTCTAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTtc                  >  1:1155748/1‑140 (MQ=255)                                                                                                                         ctctAACCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTtct                 <  2:233996/140‑1 (MQ=255)                                                                                                                              aCCACTGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGc            >  2:1031099/1‑140 (MQ=255)                                                                                                                                   tGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAttg       >  2:152192/1‑140 (MQ=255)                                                                                                                                   tGCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAttg       >  1:1291485/1‑140 (MQ=255)                                                                                                                                   tGCCAGGGCTCTATACACAATCAAGAATGANGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAttg       >  2:845594/1‑140 (MQ=255)                                                                                                                                    gCCAGGGCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGAGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAttgt      >  1:291133/1‑140 (MQ=255)                                                                                                                                        gggCTCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGAt  >  2:8678/1‑140 (MQ=255)                                                                                                                                           |                                                                                                                                         TGTCAGGGCGCGATTGTCAGAACCTTATCCCGTGGTGAAACGATTTTCTGTGACGGCACCTTTACAGGCAAAGCCGGGCGAGGTCGTTTCCTGCGACGCAAACCGTTTGTCCCTCCCGTGCTCTAACCACTGCCAGGGATCTATACACAATCAAGAATGATGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGAT  >  NC_000913/3011288‑3011562

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑