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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

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% 210.3 / NA 58Y63C (TAT→TGT) damDNA adenine methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (28/30);  total (28/30)

CCGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTATAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAATA  >  NC_000913/3515593‑3515854
                                                                                                                                     |                                                                                                                                
ccGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAgaga                                                                                                                             <  1:168167/139‑1 (MQ=255)
  gACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGCTAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTCCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACt                                                                                                                           >  2:1284750/1‑139 (MQ=255)
       aacggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCa                                                                                                                      >  2:69163/1‑139 (MQ=255)
          ggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  1:1284750/139‑1 (MQ=255)
          ggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  2:1262082/139‑1 (MQ=255)
          ggaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGt                                                                                                                   <  1:161171/139‑1 (MQ=255)
          gagacagggCTCTTGTTGGTCTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCTGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACTGTGTTACAGAGACTGATCAGGt                                                                                                                   <  1:658369/132‑1 (MQ=255)
           gaTCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTc                                                                                                                  <  2:118966/139‑1 (MQ=255)
                 ggCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTAtt                                                                                                            >  2:219842/1‑139 (MQ=255)
                     tttGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGata                                                                                                        <  1:1283963/139‑1 (MQ=255)
                      ttgttgAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGatat                                                                                                       >  1:551246/1‑139 (MQ=255)
                            aaCTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTTCGTCCTGTACGTATTCGTCAGTACGCATCTTCACAATGTTACAGATACTGAACAGGTCGCTATTGatactgtctc                                                                                                 >  2:658369/1‑132 (MQ=255)
                                 ttCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGata                                                                                            >  1:1122669/1‑139 (MQ=255)
                                  tCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGatat                                                                                           >  1:328468/1‑139 (MQ=255)
                                    gcgGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATaa                                                                                         <  2:405731/139‑1 (MQ=255)
                                           tGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGAGCAGGTCGCTATTGATATCGGCAAGGATATAACGAGaaa                                                                                  >  2:420521/1‑139 (MQ=255)
                                              tAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               <  2:1020059/139‑1 (MQ=255)
                                                gTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCg                                                                             <  2:551246/139‑1 (MQ=255)
                                                gTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCg                                                                             <  1:624223/139‑1 (MQ=255)
                                                  aaaCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCt                                                                                                               <  2:483878/103‑1 (MQ=255)
                                                  aaaCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCt                                                                                                               >  1:483878/1‑103 (MQ=255)
                                                    aCCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGgtgt                                                                         >  2:210338/1‑139 (MQ=255)
                                                      cTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATc                                                                                                      <  1:1074159/108‑1 (MQ=255)
                                                      cTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATc                                                                                                      >  2:1074159/1‑108 (MQ=255)
                                                      cTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  >  1:1283410/1‑112 (MQ=255)
                                                      cTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  <  2:1283410/112‑1 (MQ=255)
                                                       tCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTga                                                                      >  1:931398/1‑139 (MQ=255)
                                                        cGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTCCGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTgag                                                                     >  2:927590/1‑139 (MQ=255)
                                                         ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  >  2:22890/1‑109 (MQ=255)
                                                         ggCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCa                                                                                                  <  1:22890/109‑1 (MQ=255)
                                                           cgcAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGat                                                                                                         <  1:14946/100‑1 (MQ=255)
                                                           cgcAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGat                                                                                                         >  2:14946/1‑100 (MQ=255)
                                                                 ttGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGa                                                            <  1:219842/139‑1 (MQ=255)
                                                                      tCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCgg                                                       <  2:513579/139‑1 (MQ=255)
                                                                      tCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCgg                                                       <  2:456793/139‑1 (MQ=255)
                                                                      tCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCgg                                                       <  2:931398/139‑1 (MQ=255)
                                                                                   gCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAgg                                          <  2:328468/139‑1 (MQ=255)
                                                                                    cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGaaa                                                                                  <  2:790841/98‑1 (MQ=255)
                                                                                    cTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGaaa                                                                                  >  1:790841/1‑98 (MQ=255)
                                                                                        cgTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGAcc                                                          <  1:340024/118‑1 (MQ=255)
                                                                                        cgTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGAcc                                                          >  2:340024/1‑118 (MQ=255)
                                                                                         gTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGat                                                                                                         <  1:548504/70‑1 (MQ=255)
                                                                                         gTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGat                                                                                                         >  2:548504/1‑70 (MQ=255)
                                                                                                       tacTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCt                      >  2:426115/1‑139 (MQ=255)
                                                                                                        acTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCg                                                                             <  1:1127217/83‑1 (MQ=255)
                                                                                                        acTCATCAGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCg                                                                             >  2:1127217/1‑83 (MQ=255)
                                                                                                           catcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTggg                  >  2:37552/1‑139 (MQ=255)
                                                                                                            atcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGAtata                                                                                          <  2:704295/66‑1 (MQ=255)
                                                                                                            atcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGAtata                                                                                          >  1:704295/1‑66 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATc                                                                                                      >  1:358393/1‑53 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATc                                                                                                      <  2:358393/53‑1 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               >  2:157136/1‑76 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGt                                                                               <  1:157136/76‑1 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCGGACATTCGCCCTTGGGCa                >  2:1213085/1‑139 (MQ=255)
                                                                                                             tcaGTACGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCa                >  2:336915/1‑139 (MQ=255)
                                                                                                                  aCGCATCTTCACAATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGc           <  2:224819/139‑1 (MQ=255)
                                                                                                                      aTCTTCACAATGTTACAGAGACTGAACAGGTCCCTAGTCCGATCGGCGAGGTAATCACGCGAAAAATCGGTGTTGAGAAACAACGCCCCGACACCTACAAAAGGGTCCACAATAAAGTCGCCCTAGGGCCCATGCCGtt       >  2:964775/1‑139 (MQ=255)
                                                                                                                           cacaATGTTACAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAata  <  1:69163/139‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                
CCGACGGAACGGATCCTGGCTTTTGTTGAACTCTTCGCGGAACTGATAGTAAACCTCGGCGCAATTTGTTTCGGGAACAAACAGCTCGCGTGCGGCCTGTACGTACTCATCAGTACGCATCTTCACAATGTTATAGAGACTGATCAGGTCGCTATTGATATCGGCAAGGATATAACGAGAAAAGTCGGTGTTGAGAAACACCGACCCGGCACCTACAAAAGGCTCAACCAGACATTCGCCCTTGGGCAAATGCCGTTTAATA  >  NC_000913/3515593‑3515854

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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