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
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 357,791 C→T *300* (TAG→TAA)  cynR ← transcriptional activator of cyn operon, autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,7910CT98.3% 176.4 / NA 59*300* (TAG→TAA) cynRtranscriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (31/27);  total (31/28)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC  >  NC_000913/357665‑357922
                                                                                                                              |                                                                                                                                   
tCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTAACCGTGATTCa                                                                                                                         >  2:1190728/1‑139 (MQ=255)
     cAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTcc                                                                                                                    >  1:875612/1‑139 (MQ=255)
                  tGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcgcg                                                                                                       <  2:1415381/139‑1 (MQ=38)
                       gATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAttt                                                                                                  >  2:1468596/1‑139 (MQ=255)
                            ggcgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGTTCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCa                                                                                             <  2:216842/139‑1 (MQ=255)
                            ggcgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCa                                                                                             <  2:300664/139‑1 (MQ=255)
                              cgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAAc                                                                                           >  1:667801/1‑139 (MQ=255)
                                 gAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  2:1748684/139‑1 (MQ=255)
                                 gAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  2:667801/139‑1 (MQ=255)
                                          aTCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCaaa                                                                               >  2:33559/1‑139 (MQ=255)
                                                     gTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCa                                                                                                                         <  1:496691/86‑1 (MQ=255)
                                                         agCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCgcagcg                                                                >  1:1742455/1‑139 (MQ=255)
                                                         agCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCgcggcg                                                                >  2:330490/1‑139 (MQ=255)
                                                              tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        >  2:1059775/1‑110 (MQ=11)
                                                              tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  1:1059775/110‑1 (MQ=16)
                                                              tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTAc                                                                                                                                  <  2:1421452/68‑1 (MQ=255)
                                                              tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGt                                                           >  1:213202/1‑139 (MQ=255)
                                                              tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGt                                                           >  1:745770/1‑139 (MQ=255)
                                                                   tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGcc                                                      <  1:33559/139‑1 (MQ=255)
                                                                          ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGcc                                                                         >  1:1417855/1‑113 (MQ=255)
                                                                          ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGcc                                                                         <  2:1417855/113‑1 (MQ=255)
                                                                                   cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCtt                                                                       >  2:1150283/1‑106 (MQ=255)
                                                                                   cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCtt                                                                       <  1:1150283/106‑1 (MQ=255)
                                                                                   cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCtt                                                                       >  1:1726699/1‑106 (MQ=255)
                                                                                   cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCtt                                                                       <  2:1726699/106‑1 (MQ=255)
                                                                                   cGTAGCGCAACAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                      >  2:1231310/1‑139 (MQ=255)
                                                                                        cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCa                                                                                       >  2:1158093/1‑85 (MQ=11)
                                                                                        cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCtt                                                                       <  2:555950/101‑1 (MQ=11)
                                                                                        cgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCtt                                                                       >  1:555950/1‑101 (MQ=255)
                                                                                        cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCa                                                                                       <  1:1158093/85‑1 (MQ=255)
                                                                                        cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGcc                                                                         <  1:1711858/99‑1 (MQ=255)
                                                                                        cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGcc                                                                         >  2:1711858/1‑99 (MQ=255)
                                                                                        cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                 >  2:1791470/1‑139 (MQ=255)
                                                                                        cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGATTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCATTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                 >  2:1226150/1‑139 (MQ=255)
                                                                                             cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  1:740211/79‑1 (MQ=255)
                                                                                             cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        >  2:740211/1‑79 (MQ=255)
                                                                                             cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                            >  1:1273261/1‑139 (MQ=255)
                                                                                                gCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                         >  2:346369/1‑139 (MQ=255)
                                                                                                 cAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                        <  2:1273261/139‑1 (MQ=255)
                                                                                                 cAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                        <  1:1791470/139‑1 (MQ=255)
                                                                                                     tCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCAttt                                                                                                                      >  2:138042/1‑41 (MQ=255)
                                                                                                     tCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCAttt                                                                                                                      <  1:138042/41‑1 (MQ=255)
                                                                                                     tCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                    >  2:617109/1‑139 (MQ=255)
                                                                                                         gCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTcg                                                                     <  2:972355/86‑1 (MQ=255)
                                                                                                         gCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTcg                                                                     >  1:972355/1‑86 (MQ=255)
                                                                                                          ccGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        >  1:756588/1‑66 (MQ=11)
                                                                                                          ccGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  2:756588/66‑1 (MQ=11)
                                                                                                          ccGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCa               >  1:769976/1‑139 (MQ=255)
                                                                                                             cAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagta            <  1:1231310/139‑1 (MQ=255)
                                                                                                              aGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                        <  1:812284/110‑1 (MQ=255)
                                                                                                              aGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                        >  2:812284/1‑110 (MQ=255)
                                                                                                                 ccTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg        <  2:213202/139‑1 (MQ=255)
                                                                                                                      gtCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         <  2:1170024/37‑1 (MQ=255)
                                                                                                                      gtCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         >  1:1170024/1‑37 (MQ=255)
                                                                                                                       tCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAt                                                                                                    <  2:280945/41‑1 (MQ=255)
                                                                                                                       tCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAt                                                                                                    >  1:280945/1‑41 (MQ=255)
                                                                                                                       tCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc  <  2:769976/139‑1 (MQ=255)
                                                                                                                        cAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        >  2:1265256/1‑52 (MQ=255)
                                                                                                                        cAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  1:1265256/52‑1 (MQ=255)
                                                                                                                              |                                                                                                                                   
TCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC  >  NC_000913/357665‑357922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A