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 F1 I2 R1 777 59.2 2955938 92.5% 2734242 106.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,515,726 T→C Y63C (TAT→TGT)  dam ← DNA adenine methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,515,7260TC100.0% 219.1 / NA 61Y63C (TAT→TGT) damDNA adenine methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (28/33);  total (28/33)

CCGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTATAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAATA  >  NC_000913/3515593‑3515854
                                                                                                                                     |                                                                                                                                
ccGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAgaga                                                                                                                             <  2:544881/139‑1 (MQ=255)
 cGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGAc                                                                                                                            <  2:1263023/139‑1 (MQ=255)
       aacggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCa                                                                                                                      >  2:429728/1‑139 (MQ=255)
         cggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAgg                                                                                                                    >  1:987083/1‑139 (MQ=255)
          ggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  1:479707/139‑1 (MQ=255)
                tGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTAt                                                                                                             <  2:211992/139‑1 (MQ=255)
                     tttGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGata                                                                                                        <  1:585754/139‑1 (MQ=255)
                      ttgttgAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGatat                                                                                                       >  1:521834/1‑139 (MQ=255)
                         ttgAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCgg                                                                                                    <  1:303011/139‑1 (MQ=255)
                           gAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  <  2:1433656/139‑1 (MQ=255)
                           gAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  <  2:133739/139‑1 (MQ=255)
                                ctTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGat                                                                                             <  1:1180623/139‑1 (MQ=255)
                                 ttCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGata                                                                                            >  2:1325804/1‑139 (MQ=255)
                                             aTAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGAt                                                                                                                        <  1:1209397/99‑1 (MQ=255)
                                             aTAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGAt                                                                                                                        >  2:1209397/1‑99 (MQ=255)
                                             aTAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGaaaaa                                                                                >  2:374905/1‑138 (MQ=255)
                                              tAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               <  2:987083/139‑1 (MQ=255)
                                                   aaCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGgtg                                                                          <  1:429728/139‑1 (MQ=255)
                                                       tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   >  1:785637/1‑94 (MQ=255)
                                                       tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  2:785637/94‑1 (MQ=255)
                                                        cGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGc                                                                                                                <  1:464415/96‑1 (MQ=255)
                                                        cGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGc                                                                                                                >  2:464415/1‑96 (MQ=255)
                                                         ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   >  1:729993/1‑92 (MQ=255)
                                                         ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  2:729993/92‑1 (MQ=255)
                                                         ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTgaga                                                                    >  1:1246078/1‑139 (MQ=255)
                                                            gcAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGG‑‑ATAACGAGAAAAGTCGGTGTTGAGAAacac                                                               <  2:232352/139‑1 (MQ=255)
                                                                         ggAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCAc                                                    <  2:1246078/139‑1 (MQ=255)
                                                                          gAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCa                                                                                                                      >  1:1236425/1‑72 (MQ=255)
                                                                          gAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCa                                                                                                                      <  2:1236425/72‑1 (MQ=255)
                                                                                    cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGc                                         <  1:1429241/139‑1 (MQ=255)
                                                                                    cTCGCGTGCGCCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCTGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGc                                         <  1:374905/139‑1 (MQ=255)
                                                                                        cgTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGtt                                                                        <  2:1017877/104‑1 (MQ=255)
                                                                                        cgTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGtt                                                                        >  1:1017877/1‑104 (MQ=255)
                                                                                                 tGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACAtt                            <  2:521834/139‑1 (MQ=255)
                                                                                                         cTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTg                    >  2:501374/1‑139 (MQ=255)
                                                                                                           catcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTggg                  >  2:793363/1‑139 (MQ=255)
                                                                                                            atcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGc                 >  1:115719/1‑139 (MQ=255)
                                                                                                            atcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGc                 >  1:315768/1‑139 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  >  1:1030701/1‑57 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  <  2:1030701/57‑1 (MQ=255)
                                                                                                              caGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCaa               >  2:1219859/1‑139 (MQ=255)
                                                                                                                 tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCt                      <  1:353217/129‑1 (MQ=255)
                                                                                                                 tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCt                      >  2:353217/1‑129 (MQ=255)
                                                                                                                 tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            >  1:481295/1‑139 (MQ=255)
                                                                                                                 tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            >  2:760104/1‑139 (MQ=255)
                                                                                                                 tACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            <  1:760104/139‑1 (MQ=255)
                                                                                                                    gCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCg         <  1:501374/139‑1 (MQ=255)
                                                                                                                     cATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGt        <  1:1083733/139‑1 (MQ=255)
                                                                                                                      aTCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            >  1:1307367/1‑134 (MQ=255)
                                                                                                                      aTCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATg            <  2:1307367/134‑1 (MQ=255)
                                                                                                                      aTCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGtt       <  2:315768/139‑1 (MQ=255)
                                                                                                                      aTCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGtt       >  2:747635/1‑139 (MQ=255)
                                                                                                                           cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACAtt                            <  2:144533/113‑1 (MQ=255)
                                                                                                                           cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACAtt                            >  1:144533/1‑113 (MQ=255)
                                                                                                                           cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAata  >  1:12069/1‑139 (MQ=255)
                                                                                                                                tGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               >  2:533864/1‑57 (MQ=255)
                                                                                                                                tGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               <  1:533864/57‑1 (MQ=255)
                                                                                                                                tGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGgtg                                                                          >  2:78499/1‑62 (MQ=255)
                                                                                                                                tGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGgtg                                                                          <  1:78499/62‑1 (MQ=255)
                                                                                                                                tGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACAtt                            >  2:436265/1‑108 (MQ=255)
                                                                                                                                tGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACAtt                            <  1:436265/108‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                
CCGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTATAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAATA  >  NC_000913/3515593‑3515854

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A