Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A43 F60 I1 R1 21 74.4 2534558 98.9% 2506677 138.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8791.C93.8% 162.0 / 3.0 48coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (3/0);  new base C (20/25);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 1.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑CCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGA  >  NC_000913/3815741‑3816009
                                                                                                                                            |                                                                                                                                    
cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgat‑t‑c                                                                                                                                     <  1:102990/140‑1 (MQ=255)
  aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑ccc                                                                                                                                   >  1:708606/1‑140 (MQ=255)
     aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑ccc‑cct                                                                                                                               <  2:659139/140‑3 (MQ=255)
     aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑ccc‑cct                                                                                                                               <  2:624205/140‑3 (MQ=255)
         ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑ccc‑cct                                                                                                                               >  1:172016/1‑134 (MQ=255)
         ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCACTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑ccc‑cct                                                                                                                               <  2:172016/136‑3 (MQ=255)
          cagcTGATATGGTTTCACGCCTCCGCTCCTCCTCTTACTTTTCTACAGGCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGc                                                                                                                          <  2:511342/138‑1 (MQ=255)
           cgcTGATATGGTTTCATGCCTTAGCCCCTTATCTTACCTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGcc                                                                                                                         <  1:364416/140‑1 (MQ=255)
                atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGc                                                                                                                    >  2:1230806/1‑140 (MQ=255)
                  atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCca                                                                                                                  <  1:780251/140‑1 (MQ=255)
                    ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCGTTCTGCGTGGCTACAATGGATTCGAG‑T‑CCCAC‑TCGGGCCAGAGCcaac                                                                                                                >  2:364416/1‑140 (MQ=255)
                       ttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                             <  2:1207785/140‑1 (MQ=255)
                        tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATAC‑CCC‑C‑TCGGACCAGAGCcaacactg                                                                                                            >  1:511342/1‑137 (MQ=255)
                          attccTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                          >  2:808050/4‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTATAATTCAGTTTGCCAGCGCCGCCTTCTGCGTAGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGCTg                                                                                                          >  2:1152468/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                          >  2:992981/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                          >  1:1053941/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAAGGATTCGCT‑T‑CCC‑CATCGGGCCAGAGCCAACAAGATg                                                                                                          >  1:513021/1‑140 (MQ=255)
                            gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAg                                                                                                        <  2:958705/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACTGACAAAAAAAACGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  1:549230/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  1:1230806/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  1:992981/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACGTTTCTACAGACAAAAAATAGGAGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  2:476324/140‑1 (MQ=255)
                                tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCcaac                                                                                                                >  1:20199/1‑128 (MQ=255)
                                tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCcaac                                                                                                                <  2:20199/128‑1 (MQ=255)
                                 cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                   >  1:31439/1‑140 (MQ=255)
                                    tcctcATCTTACTTTTCTACAGTCAAAAAAAAGGCGACTTATCAGTCGTCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                <  2:532958/140‑1 (MQ=255)
                                    tcctcATCTTACTTTTCCACAGACAAAAAAATGGCTACTGATCAGTCGCCTTAAAAATTAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                <  2:371597/140‑1 (MQ=255)
                                       tcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCAt                                                                                             >  1:57658/1‑140 (MQ=255)
                                        cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGTTTCGAT‑TCCCC‑C‑CCGGGCCAGAGCCAACAACATGAGTAGCTCTTCATg                                                                                            >  2:527044/1‑140 (MQ=255)
                                        cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATg                                                                                            >  2:1087977/1‑140 (MQ=255)
                                          tCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑ACGGGCCAGAGCTAACAAGATGAGTAGCTCTTCATggg                                                                                          >  1:476324/1‑140 (MQ=255)
                                               cTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                                                     <  1:760407/140‑1 (MQ=255)
                                                    cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                                <  1:1087977/140‑1 (MQ=255)
                                                         gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                           >  1:1016740/1‑140 (MQ=255)
                                                              aaaaaaGGCGACTCACCAGTCGGCTTAAATATCAGTTCGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                      <  1:358929/140‑1 (MQ=255)
                                                                    ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                <  1:1123864/140‑1 (MQ=255)
                                                                      cGACTCATCAGTCGCCTTAAAAATCAGTTTGCTAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  2:771372/140‑1 (MQ=255)
                                                                        aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGcc                                                            >  2:81248/1‑139 (MQ=255)
                                                                        aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                            <  1:893589/140‑1 (MQ=255)
                                                                                   gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                 >  1:1033620/1‑140 (MQ=255)
                                                                                      ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                              >  1:1121994/1‑140 (MQ=255)
                                                                                        aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgcac                                            >  2:787700/1‑138 (MQ=255)
                                                                                            aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                        <  2:727862/140‑1 (MQ=255)
                                                                                            aTCAGTTTGCCAGCGCCCCCTTCTGCGTCGCGACACTGGTTTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                        <  2:513021/140‑1 (MQ=255)
                                                                                                 tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCACGTCTTCGGt                                   <  1:787700/140‑1 (MQ=255)
                                                                                                  ttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtc                                  >  2:1229616/1‑140 (MQ=255)
                                                                                                   tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                 <  2:1121994/140‑1 (MQ=255)
                                                                                                      cAGCGCCGCCTTCTGAGTCGCTTCACTGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                              <  1:527044/140‑1 (MQ=255)
                                                                                                           ccgccTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACg                         >  1:1107677/1‑140 (MQ=255)
                                                                                                             gccTTCTGCGTCGCTACAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGtt                       <  1:1187752/140‑1 (MQ=255)
                                                                                                                            aCAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCGCGTCTTCTGTCGTCGCTACGTACATGTCGGTCTCTGc        >  1:390416/1‑140 (MQ=255)
                                                                                                                            aCAATGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCAGTCTTCACTACGTGCATGTCGGTCTCTGc        >  1:569953/1‑140 (MQ=255)
                                                                                                                                tGGATTCGAT‑TCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa    <  2:1053941/140‑1 (MQ=255)
                                                                                                                                  gattcgat‑tcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga  <  2:708606/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                    
CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑CCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGA  >  NC_000913/3815741‑3816009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A