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
A3 F60 I1 R1 14 93.5 3190714 98.8% 3152425 138.6

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.C87.5% 125.7 / 10.2 40coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (4/1);  new base C (12/23);  total (16/24)
Fisher's exact test for biased strand distribution p-value = 1.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑C‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815743‑3816012
                                                                                                                                           |                                                                                                                                        
aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑c‑cc                                                                                                                                      >  1:1030350/1‑140 (MQ=255)
 tAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGGGCCGCCTGCTGTGTAGCTACAATGGATTCGA‑TT‑c‑cc‑c                                                                                                                                    >  1:566682/1‑140 (MQ=255)
   aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑c‑cc‑cct                                                                                                                                  <  2:1084832/140‑3 (MQ=255)
         cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGcc                                                                                                                            >  2:366831/1‑140 (MQ=255)
               tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGcc                                                                                                                      <  1:215277/140‑1 (MQ=255)
                     ttCATGCCTTCGCTCGTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                                <  1:648564/140‑1 (MQ=255)
                     ttCATGCCTTCGCTCCTGATCTGACTTTTCTCCAGCC‑AACAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                                <  2:482466/140‑1 (MQ=255)
                        aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGTATTCGA‑TT‑C‑CC‑CGTCGGTCCAGAGCCAACAAGATg                                                                                                             >  2:634900/1‑140 (MQ=255)
                            cTTCGCTCCTCATCTCACTTTTTTACAGAC‑‑AAAAAAATGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:504024/140‑1 (MQ=255)
                             ttCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGt                                                                                                          <  2:1135323/138‑1 (MQ=255)
                             ttCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGt                                                                                                          >  1:1135323/1‑138 (MQ=255)
                             ttCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:234662/140‑1 (MQ=255)
                              tCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTTGA‑TT‑C‑CCGC‑TCGGGCCAGAGCGAACAAGATGAGTAGc                                                                                                       >  1:482466/1‑140 (MQ=255)
                              tCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGAATCGC‑TT‑CTCC‑C‑TCGGGGCAGAGCCAACAAGATGAGTAGc                                                                                                       >  2:774025/1‑140 (MQ=255)
                               cGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                                <  1:328136/130‑1 (MQ=255)
                               cGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                                >  2:328136/1‑130 (MQ=255)
                               cGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                      <  1:366831/140‑1 (MQ=255)
                                      cATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑C‑CCAC‑TCGGGCAAGATCCTACAAGACGAGTAGCTCTTCATg                                                                                               >  1:723590/1‑140 (MQ=255)
                                            aCTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                         >  2:1383857/1‑140 (MQ=255)
                                             cTTTTCTACAGAC‑AAAAAAAAGTCGCCTCATCAGTCGTCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                                                        <  1:537429/140‑1 (MQ=255)
                                              ttttCTACAGACAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                                                        <  2:1400352/140‑1 (MQ=255)
                                                ttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                     >  1:306936/1‑140 (MQ=255)
                                                ttCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                     >  2:108786/1‑140 (MQ=255)
                                                       gAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                              <  2:1030350/140‑1 (MQ=255)
                                                             aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  2:153256/140‑1 (MQ=255)
                                                             aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  1:224897/140‑1 (MQ=255)
                                                                   ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                   <  1:286791/140‑1 (MQ=255)
                                                                     cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 >  2:1353762/1‑140 (MQ=255)
                                                                     cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  1:1353762/140‑1 (MQ=255)
                                                                     cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCCCCTTCTGCTTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:566682/140‑1 (MQ=255)
                                                                       aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                               <  1:74552/140‑1 (MQ=255)
                                                                       aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                               <  2:306936/140‑1 (MQ=255)
                                                                                     ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:163542/1‑140 (MQ=255)
                                                                                     ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGACCCCTGAACTTCAATGATgcgc                                                 >  1:749069/1‑140 (MQ=255)
                                                                                            tCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                          <  2:163542/140‑1 (MQ=255)
                                                                                            tCAGTTTGCCAGCGCCACCTTCTGCGTCGCGACGATGGACTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                          <  2:749069/140‑1 (MQ=255)
                                                                                              aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        >  1:1338833/1‑140 (MQ=255)
                                                                                              aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        <  2:318166/140‑1 (MQ=255)
                                                                                              aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        >  1:1492403/1‑140 (MQ=255)
                                                                                                tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                      >  1:965905/1‑140 (MQ=255)
                                                                                                  tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                    <  2:965905/140‑1 (MQ=255)
                                                                                                   gCCAGCGCCGCCTTCTGTGTCGGTACAATGGGTTCCATTT‑C‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                   <  2:593196/140‑1 (MQ=255)
                                                                                                                               tGGATTCGA‑TTCC‑CC‑C‑TCGGGCCAGGGCCTACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa       <  1:634900/140‑1 (MQ=255)
                                                                                                                                 gattcga‑ttcC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     >  1:1122286/1‑140 (MQ=255)
                                                                                                                                    tcga‑ttcC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct             <  2:207728/129‑1 (MQ=255)
                                                                                                                                    tcga‑ttcC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct             >  1:207728/1‑129 (MQ=255)
                                                                                                                                    tcga‑ttcC‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCCCCCGTCTTCGGTCAACACTACGTTCCTGTCGATCTCTGCGGCAGAGTc  >  2:717801/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                        
ATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGA‑TT‑C‑CC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815743‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A