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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,838,137 G→A *395* (TAG→TAA)  setC → putative arabinose efflux transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,838,1370GA100.0% 179.8 / NA 57*395* (TAG→TAA) setCputative arabinose efflux transporter
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/26);  total (31/26)

CACGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAGCTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGG  >  NC_000913/3838001‑3838268
                                                                                                                                        |                                                                                                                                   
cACGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACt                                                                                                                                   >  1:922136/1‑139 (MQ=255)
  cgcgTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCa                                                                                                                                 <  1:1131775/139‑1 (MQ=255)
                   cGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGaa                                                                                                                >  1:613193/1‑139 (MQ=255)
                           ctGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGc                                                                                                        <  2:58699/139‑1 (MQ=255)
                                 aCGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGgcg                                                                                                  <  1:1490359/139‑1 (MQ=255)
                                          tGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGGTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACagag                                                                                         >  2:122123/1‑139 (MQ=255)
                                            gtcgAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTggg                                                                                                                       <  1:984810/104‑1 (MQ=255)
                                            gTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGATTATTAAAGATATTTAACTCACCAGTCTggg                                                                                                                       >  2:984810/1‑107 (MQ=255)
                                                      ggAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAAt                                                                                                            >  2:835961/1‑108 (MQ=255)
                                                      ggAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAAt                                                                                                            <  1:835961/108‑1 (MQ=255)
                                                                tGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                   <  2:922136/139‑1 (MQ=255)
                                                                  cGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCa                                                                 >  1:1179681/1‑139 (MQ=255)
                                                                  cGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCa                                                                 >  1:960532/1‑139 (MQ=255)
                                                                   gttgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCAt                                                                <  2:1217225/139‑1 (MQ=255)
                                                                   gttgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCAt                                                                <  2:960532/139‑1 (MQ=255)
                                                                     tgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              >  2:867376/1‑107 (MQ=255)
                                                                     tgttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              <  1:867376/107‑1 (MQ=255)
                                                                       ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                        <  1:338713/127‑1 (MQ=255)
                                                                       ttCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                        >  2:338713/1‑127 (MQ=255)
                                                                        tCTGGCTGGCGATAGGGATGTTGGGTATTGCTATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              <  1:182175/104‑1 (MQ=255)
                                                                        tCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              >  2:182175/1‑104 (MQ=255)
                                                                          tggctggcGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAATAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGca                                                         >  1:962763/1‑139 (MQ=255)
                                                                                 cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGca                                                         <  1:745328/132‑1 (MQ=255)
                                                                                 cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGca                                                         >  2:745328/1‑132 (MQ=255)
                                                                                 cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATaa                                                  >  2:487022/1‑139 (MQ=255)
                                                                                 cGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATaa                                                  >  2:771022/1‑139 (MQ=255)
                                                                                     aGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGa                                              <  2:1179681/139‑1 (MQ=255)
                                                                                       ggATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            <  2:962763/139‑1 (MQ=255)
                                                                                          tGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGt                                                                                                                            <  1:1344095/56‑1 (MQ=255)
                                                                                          tGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGt                                                                                                                            >  2:1344095/1‑56 (MQ=255)
                                                                                           gTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                               >  2:1331876/1‑116 (MQ=255)
                                                                                           gTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                               <  1:1331876/116‑1 (MQ=255)
                                                                                           gTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAAc                                        >  2:1071507/1‑139 (MQ=255)
                                                                                              gggTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGt                                     >  2:156474/1‑139 (MQ=255)
                                                                                                   ttGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACagag                                                                                         >  2:800936/1‑82 (MQ=255)
                                                                                                   ttGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACagag                                                                                         <  1:800936/82‑1 (MQ=255)
                                                                                                   ttGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                        <  1:266332/99‑1 (MQ=255)
                                                                                                   ttGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCAttttt                                                                        >  2:266332/1‑99 (MQ=255)
                                                                                                     gCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                               <  2:1456597/106‑1 (MQ=255)
                                                                                                     gCGATGATTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATg                                                               >  1:1456597/1‑106 (MQ=255)
                                                                                                           atTTGCCTGCTGTTTATTAAAGATATTTTACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCCTCCTTGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            <  2:1525206/119‑1 (MQ=255)
                                                                                                           atTTGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACa                                            >  1:1525206/1‑119 (MQ=255)
                                                                                                              tGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                   >  2:279624/1‑93 (MQ=255)
                                                                                                              tGCCTGCTGTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTAt                                                                   <  1:279624/93‑1 (MQ=255)
                                                                                                                   gctgTTTATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGtt                >  2:1351371/1‑139 (MQ=255)
                                                                                                                       tttATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTg                                                                       >  1:712855/1‑80 (MQ=255)
                                                                                                                       tttATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTg                                                                       <  2:712855/80‑1 (MQ=255)
                                                                                                                       tttATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCt                                                            <  2:652231/91‑1 (MQ=255)
                                                                                                                       tttATTAAAGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCt                                                            >  1:652231/1‑91 (MQ=255)
                                                                                                                               aGATATTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgg    >  2:1475760/1‑139 (MQ=255)
                                                                                                                                 atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCa                                                                 >  2:451133/1‑76 (MQ=255)
                                                                                                                                 atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCa                                                                 <  1:451133/76‑1 (MQ=255)
                                                                                                                                 atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgggg  >  1:583306/1‑139 (MQ=255)
                                                                                                                                 atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAgggg  >  1:93423/1‑139 (MQ=255)
                                                                                                                                 atatTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCCTGGCGGAAACAGGGCCATCCTCGGCATTTTTGCTATCATGCCTGCATACATAAACGAAAAAACAGTATTCAGAGGGAAAAATGGGTTCCACCAGAAAgggg  <  1:771022/139‑1 (MQ=255)
                                                                                                                                   atTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              >  2:574097/1‑45 (MQ=255)
                                                                                                                                   atTTAACTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCaaa                                                                                              <  1:574097/45‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                   
CACGCGTCGGCTGGATTATCGCCGGCTCTGTTGACGGAATTATGGTTGAAATCTGGAGCTACCATGCGTTGTTCTGGCTGGCGATAGGGATGTTGGGTATTGCGATGATTTGCCTGCTGTTTATTAAAGATATTTAGCTCACCAGTCTGGGCTAAGAAAAATCGGCGTGGCGCAAACAGAGCCATCCTCGCCATTTTTGCTATCATGCCTGCATACATAAACGACAAAACAGTATGCAGAGGGAAAAATGGGTTCCACCAGAAAGGGG  >  NC_000913/3838001‑3838268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A