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
A6 F1 I1 R1 750 51.0 2595496 93.6% 2429384 106.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,176,858 C→T *141* (TAG→TAA)  yqiB ← DUF1249 protein YqiB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,176,8580CT100.0% 183.6 / NA 58*141* (TAG→TAA) yqiBDUF1249 protein YqiB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/26);  total (32/26)

GTTTACCCCTAACAGGGCTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGCTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATACCGCGCTTTGAA  >  NC_000913/3176723‑3176989
                                                                                                                                       |                                                                                                                                   
gtTTACCCCTAACAGGGCTACGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTtaa                                                                                                                                  >  1:486446/1‑139 (MQ=255)
           aCAGGGCTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATACTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCATAGGTTTCACGACGTTAATAAACCGGAAt                                                                                                                       >  1:876116/1‑139 (MQ=255)
                gCTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCa                                                                                                                  >  2:474279/1‑139 (MQ=255)
                gCTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCa                                                                                                                  >  1:416221/1‑139 (MQ=255)
                gCTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTCGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCa                                                                                                                  >  2:982124/1‑139 (MQ=255)
                gCTCCGTGCTTTTGTGCAAACAGGTGAGCGTCGCTACTATCTACAACCCCGACTCTTGCATCACCCAACAGAGGTAGGGTTAACAGGCTTCCCAAATGATGTCCTTAGATTTCACCACGTAAATAAACCGGACTCGCCa                                                                                                                  >  2:268769/1‑139 (MQ=255)
                 cTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCAt                                                                                                                 >  2:1241401/1‑139 (MQ=255)
                   tCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCg                                                                                                               <  1:474279/139‑1 (MQ=255)
                    cGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGc                                                                                                              >  2:1129980/1‑139 (MQ=255)
                       gCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTcc                                                                                                           <  1:1230844/139‑1 (MQ=255)
                        cTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTCGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCa                                                                                                          <  1:982124/139‑1 (MQ=255)
                          tttGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCAtg                                                                                                        <  2:416221/139‑1 (MQ=255)
                              tgCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCt                                                                                                    >  1:568489/1‑139 (MQ=255)
                                cAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTaa                                                                                                  >  1:427071/1‑139 (MQ=255)
                                cAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTaa                                                                                                  >  1:469662/1‑139 (MQ=255)
                                 aaaCAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTaaa                                                                                                 <  2:427071/139‑1 (MQ=255)
                                      ggTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTa                                                                                            >  1:327398/1‑139 (MQ=255)
                                        tGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACa                                                                                               >  2:618643/1‑134 (MQ=255)
                                        tGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACa                                                                                               <  1:618643/134‑1 (MQ=255)
                                               cGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCa                                                                                   >  1:286735/1‑139 (MQ=255)
                                                                cTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGAt                                                                  <  2:568489/139‑1 (MQ=255)
                                                                   aCTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCAtgtg                                                                                                      >  1:1170922/1‑100 (MQ=255)
                                                                   aCTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCAtgtg                                                                                                      <  2:1170922/100‑1 (MQ=255)
                                                                       tGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTcc                                                                                                           >  1:208664/1‑91 (MQ=255)
                                                                       tGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTcc                                                                                                           <  2:208664/91‑1 (MQ=255)
                                                                       tGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTg                                                           <  2:1159533/139‑1 (MQ=255)
                                                                                    cagAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTtcgtcg                                              >  2:771441/1‑139 (MQ=255)
                                                                                                 aaCAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTcc                                                                                                           >  2:950858/1‑65 (MQ=255)
                                                                                                 aaCAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTcc                                                                                                           <  1:950858/65‑1 (MQ=255)
                                                                                                        tttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTttatt                          <  1:733501/139‑1 (MQ=255)
                                                                                                        tttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTttatt                          <  2:51360/139‑1 (MQ=255)
                                                                                                        tttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAA‑TTGATGCTTTTCGTCGCGTTGATGCAACTTTttatta                         >  1:327301/1‑139 (MQ=255)
                                                                                                         ttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGcc                                                                                                                   >  1:704518/1‑49 (MQ=255)
                                                                                                         ttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGcc                                                                                                                   <  2:704518/49‑1 (MQ=255)
                                                                                                         ttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTttatta                         >  1:1016932/1‑139 (MQ=255)
                                                                                                         ttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTttatta                         >  2:85774/1‑139 (MQ=255)
                                                                                                         ttCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAA‑TTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAg                        <  2:327301/139‑1 (MQ=255)
                                                                                                          tCCAATTTGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTTCTAAACAGTATCGCAACCAGTACGCTAAAAACTGATTAATTTGATGCTTGTCGTCGCGTTGATGCAACTTTTTATTAg                        <  1:995703/139‑1 (MQ=255)
                                                                                                          tCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAg                        <  1:85774/139‑1 (MQ=255)
                                                                                                          tCCAAATGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTACATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGCTTAATTTGCTGCTTTTCGTCGCGTTGATGCAACTTTTTATTAg                        <  2:1016932/139‑1 (MQ=255)
                                                                                                               aTGGTGTCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATaa                   <  2:286735/139‑1 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATTGCCATCGCTCCATGTGCTAAACAGTGTCGCAACCAGTCCGCTAAAAACTGATTAATTCGATGCTCTtcg                                                 <  2:751432/104‑1 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCg                                                                                                               <  2:515444/42‑1 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCg                                                                                                               >  1:515444/1‑42 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAAGAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATa              <  1:1129619/139‑1 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTGTCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTtcg                                                 >  1:751432/1‑104 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAACCTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATa              >  2:1129619/1‑139 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGc                                     <  1:60631/116‑1 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGc                                     >  2:60631/1‑116 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAg                        >  1:1102368/1‑129 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAg                        <  2:1102368/129‑1 (MQ=255)
                                                                                                                    gtCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATa              >  1:1022769/1‑139 (MQ=255)
                                                                                                                     tCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCAtgtg                                                                                                      <  1:463209/50‑1 (MQ=255)
                                                                                                                     tCCTTAGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCAtgtg                                                                                                      >  2:463209/1‑50 (MQ=255)
                                                                                                                          aGGTTTCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATACCgcgc        >  2:251045/1‑139 (MQ=255)
                                                                                                                             tttCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTAt                                                                                           >  1:1116294/1‑53 (MQ=255)
                                                                                                                             tttCACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTAt                                                                                           <  2:1116294/53‑1 (MQ=255)
                                                                                                                                cACGACGTTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATACCGCGCTTTGaa  >  1:371266/1‑139 (MQ=255)
                                                                                                                                       |                                                                                                                                   
GTTTACCCCTAACAGGGCTTCGTGCTTTTGTGCAAACAGGTGAGTGTCGGTAATTTGTAAAATCCTGACTCTGGCCTCACCAGCCAGAGGAAGGGTTAACAGGCTTTCCAAATGGTGTCCTTAGGTTTCACGACGCTAATAAACCGGAATCGCCATCGCTCCATGTGCTAAACAGTATCGCAACCAGTCCGCTAAAAACTGATTAATTTGATGCTTTTCGTCGCGTTGATGCAACTTTTTATTAGGATAATCATACCGCGCTTTGAA  >  NC_000913/3176723‑3176989

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A