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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,976,605 T→C F110L (TTT→CTT)  wzxE → O‑antigen translocase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,976,6050TC100.0% 197.6 / NA 55F110L (TTT→CTT) wzxEO‑antigen translocase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/28);  total (27/28)

TACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGTTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGTT  >  NC_000913/3976470‑3976726
                                                                                                                                       |                                                                                                                          
tACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTg                                                                                                                         >  1:1343783/1‑139 (MQ=255)
          aGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGa                                                                                                               <  2:1369919/139‑1 (MQ=255)
               cATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATc                                                                                                          >  2:1258611/1‑139 (MQ=255)
                 tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGa                                                                                                               <  2:642334/132‑1 (MQ=255)
                 tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGa                                                                                                               >  1:642334/1‑132 (MQ=255)
                 tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATc                                                                                                          <  2:657276/137‑1 (MQ=255)
                 tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATc                                                                                                          >  1:657276/1‑137 (MQ=255)
                 tGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑g                                                                                                       >  2:302672/1‑139 (MQ=255)
                    tAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑gggg                                                                                                    <  2:450037/139‑1 (MQ=255)
                      aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGc                                                                                                   <  2:1413029/138‑1 (MQ=255)
                      aTCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGc                                                                                                   >  1:1413029/1‑138 (MQ=255)
                         cGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGt                                                                                               <  2:1343783/139‑1 (MQ=255)
                                            ggTCGGCACTTCATCATCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTCGTg                                                                            <  2:1136466/139‑1 (MQ=255)
                                                     ttCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATgggg                                                                   <  1:302672/139‑1 (MQ=255)
                                                      tcatcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGa                                                                  <  1:1258611/139‑1 (MQ=255)
                                                       catcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGAt                                                                 >  1:897078/1‑139 (MQ=255)
                                                        atcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATc                                                                >  1:1422777/1‑139 (MQ=255)
                                                        atcaGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATc                                                                >  2:955834/1‑139 (MQ=255)
                                                               aTGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                            >  2:80120/1‑120 (MQ=255)
                                                               aTGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                            <  1:80120/120‑1 (MQ=255)
                                                               aTGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTggg                                                         >  2:1643075/1‑139 (MQ=255)
                                                                tGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTgggg                                                        <  2:1422777/139‑1 (MQ=255)
                                                                 ggTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGACTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAATTGGGGATCGCCTGGGGc                                                       <  1:955834/139‑1 (MQ=255)
                                                                   tACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                            >  2:682822/1‑116 (MQ=255)
                                                                   tACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                            <  1:682822/116‑1 (MQ=255)
                                                                   tACTTGGTTTCTCTACGCTGATGGCGCTGGGTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTACCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCaa                                                     >  1:103716/1‑139 (MQ=255)
                                                                    aCTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAAc                                                    <  2:201217/139‑1 (MQ=255)
                                                                          tttCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                            >  2:1413467/1‑110 (MQ=255)
                                                                          tttCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCAGGGGGCTGGTGCGTTTAGTGGCGCTGGTg                                                                            <  1:1413467/110‑1 (MQ=255)
                                                                          tttCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGt                                                                                               >  2:703699/1‑90 (MQ=255)
                                                                          tttCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGt                                                                                               <  1:703699/90‑1 (MQ=255)
                                                                             ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGa                                                                                                               <  2:1609666/72‑1 (MQ=255)
                                                                             ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGa                                                                                                               >  1:1609666/1‑72 (MQ=255)
                                                                             ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCaaa                                                                        >  1:977216/1‑110 (MQ=255)
                                                                             ctctACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCaaa                                                                        <  2:977216/110‑1 (MQ=255)
                                                                                       aTGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCt                                                            <  2:257773/112‑1 (MQ=255)
                                                                                       aTGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCt                                                            >  1:257773/1‑112 (MQ=255)
                                                                                       aTGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCtgatga                                 <  2:897078/139‑1 (MQ=255)
                                                                                        tGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGaa                                >  1:1195166/1‑139 (MQ=255)
                                                                                             cTGGTTTTTGTGTTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑gggg                                                                                                    >  1:914478/1‑66 (MQ=255)
                                                                                             cTGGTTTTTGTGTTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑gggg                                                                                                    <  2:914478/66‑1 (MQ=255)
                                                                                                     tgtgCTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGAt                   <  2:411861/139‑1 (MQ=255)
                                                                                                         cTGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCg               <  2:1195166/139‑1 (MQ=255)
                                                                                                          tGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGt                                                                                      <  1:515714/67‑1 (MQ=255)
                                                                                                          tGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGt                                                                                      >  2:515714/1‑67 (MQ=255)
                                                                                                          tGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTgggg                                                        >  2:981063/1‑97 (MQ=255)
                                                                                                          tGGCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTgggg                                                        <  1:981063/97‑1 (MQ=255)
                                                                                                           ggCAGCTGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCa             >  2:1310270/1‑139 (MQ=255)
                                                                                                                 tGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTcgc                      >  2:1601952/1‑124 (MQ=255)
                                                                                                                 tGCGCCAATCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTcgc                      <  1:1601952/124‑1 (MQ=255)
                                                                                                                      cAATCAGCCAGGGATTGCTTGGTAACACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGtt  >  1:775545/1‑139 (MQ=255)
                                                                                                                        aTCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCt                                      <  2:1230383/101‑1 (MQ=255)
                                                                                                                        aTCAGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCt                                      >  1:1230383/1‑101 (MQ=255)
                                                                                                                           aGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGc                                                       >  2:420307/1‑81 (MQ=255)
                                                                                                                           aGCCAGGGATTGCTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGc                                                       <  1:420307/81‑1 (MQ=255)
                                                                                                                                       |                                                                                                                          
TACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGCGTGGTCGGCACTTCATCAGCGATGGTACTTGGTTTCTCTACGCTGATGGCGCTGGTTTTTGTGCTGGCAGCTGCGCCAATCAGCCAGGGATTGTTTGGTAATACCGACTATCA‑GGGGCTGGTGCGTTTAGTGGCGCTGGTGCAAATGGGGATCGCCTGGGGCAACCTGTTACTGGCGCTGATGAAAGGCTTTCGCGATGCCGCAGGTAATGCGTT  >  NC_000913/3976470‑3976726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A