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
A11 F1 I2 R1 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,964,697 G→A L118L (CTC→CTT)  flhA ← putative flagellar export pore protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,964,6970GA100.0% 178.4 / NA 55L118L (CTC→CTT) flhAputative flagellar export pore protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/24);  total (31/24)

ATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAA  >  NC_000913/1964572‑1964821
                                                                                                                              |                                                                                                                            
aTACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAAATGAAAAACACCACGATACCGAAAGGGAAATTGCCACAAAAAAGGAAGTGACCg                                                                                                                  >  2:1419172/1‑139 (MQ=255)
       cGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTc                                                                                                          >  2:1116552/1‑139 (MQ=255)
           aaCAAAGCGCCCAACCACTTCTGCGATACCCCCGGCACCCTTGGTAAATACCCAAAAGGTGATGATCACGAGAAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGac                                                                                                       <  1:1419172/139‑1 (MQ=255)
                                 gCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                                <  1:1227661/107‑1 (MQ=255)
                                 gCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                                >  2:1227661/1‑107 (MQ=255)
                                 gCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgc                                                                                >  2:265104/1‑139 (MQ=255)
                                 gCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgc                                                                                <  1:1562309/139‑1 (MQ=255)
                                       cGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTAt                                                                          >  2:125548/1‑139 (MQ=255)
                                       cGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACAACCTTCCCTGCCGCCGCCGCGCCGGTAt                                                                          >  2:77293/1‑139 (MQ=255)
                                         cccGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGc                                                                        >  1:183459/1‑139 (MQ=255)
                                            ggCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCt                                                                     <  1:1116552/139‑1 (MQ=255)
                                                        aaTGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCt                                                                     <  2:854521/127‑1 (MQ=255)
                                                        aaTGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCt                                                                     >  1:854521/1‑127 (MQ=255)
                                                        aaTGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATg                                                         >  1:403975/1‑139 (MQ=255)
                                                           gACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                                 <  2:1290517/112‑1 (MQ=255)
                                                           gACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                                 >  1:1290517/1‑112 (MQ=255)
                                                           gACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATa                                                      <  2:870418/139‑1 (MQ=255)
                                                            aCCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATAc                                                     >  1:21350/1‑139 (MQ=255)
                                                                    gTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGaa                                             <  1:265104/139‑1 (MQ=255)
                                                                        atgatCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                         >  1:576746/1‑139 (MQ=255)
                                                                        atgatCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                         >  1:842112/1‑139 (MQ=255)
                                                                        atgatCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                         <  2:183459/139‑1 (MQ=255)
                                                                        atgatCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCa                                         >  2:144858/1‑139 (MQ=255)
                                                                           atCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACg                                                                                                              >  1:447888/1‑67 (MQ=255)
                                                                           atCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACg                                                                                                              <  2:447888/67‑1 (MQ=255)
                                                                            tCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGtt                                     >  2:565147/1‑139 (MQ=255)
                                                                               cGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGa                                                                                                                          >  2:315819/1‑51 (MQ=255)
                                                                               cGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGa                                                                                                                          <  1:315819/51‑1 (MQ=255)
                                                                               cGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTc                                                                   <  2:353452/106‑1 (MQ=255)
                                                                               cGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTc                                                                   >  1:353452/1‑106 (MQ=255)
                                                                                 ag‑aATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTg                                <  1:125548/139‑1 (MQ=255)
                                                                                      tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                                >  1:460412/1‑103 (MQ=255)
                                                                                      tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                                <  2:460412/103‑1 (MQ=255)
                                                                                      tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAg                            >  2:1424800/1‑139 (MQ=255)
                                                                                           aaCACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCa                       >  1:1112833/1‑139 (MQ=255)
                                                                                            acacCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa                      <  2:1112833/139‑1 (MQ=255)
                                                                                              accacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACa                    >  1:813610/1‑139 (MQ=255)
                                                                                               ccacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAg                   >  2:866766/1‑139 (MQ=255)
                                                                                                 acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATa                                                      <  1:486442/102‑1 (MQ=255)
                                                                                                 acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATa                                                      >  2:486442/1‑102 (MQ=255)
                                                                                                 acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTg                                               >  1:658931/1‑109 (MQ=255)
                                                                                                 acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTg                                               <  2:658931/109‑1 (MQ=255)
                                                                                                 acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCg                 <  1:144858/139‑1 (MQ=255)
                                                                                                 acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCg                 <  2:576746/139‑1 (MQ=255)
                                                                                                  cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgccgc                                                                                     <  2:388792/70‑1 (MQ=255)
                                                                                                  cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgccgc                                                                                     >  1:388792/1‑70 (MQ=255)
                                                                                                  cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGt                >  1:252020/1‑139 (MQ=255)
                                                                                                        cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTaaa          >  2:1496919/1‑139 (MQ=255)
                                                                                                        cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAACGTGGTaaa          <  2:691214/139‑1 (MQ=255)
                                                                                                          aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCa                                                                 <  1:1120178/82‑1 (MQ=255)
                                                                                                          aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCa                                                                 >  2:1120178/1‑82 (MQ=255)
                                                                                                          aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAaaca        >  2:1356767/1‑139 (MQ=255)
                                                                                                          aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAaaca        >  1:257084/1‑139 (MQ=255)
                                                                                                           tAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAaacaa       <  2:842112/139‑1 (MQ=255)
                                                                                                             gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAacaaca     >  1:894931/1‑139 (MQ=255)
                                                                                                                aaaTTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTTAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGaa  <  2:21350/139‑1 (MQ=255)
                                                                                                                              |                                                                                                                            
ATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAG‑AATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAA  >  NC_000913/1964572‑1964821

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