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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 980,848 (A)6→5 intergenic (+62/‑199) mukB → / → ldtD chromosome condensin MukBEF, ATPase and DNA‑binding subunit/murein L,D‑transpeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913980,8430A.100.0% 117.5 / NA 29intergenic (+57/‑204)mukB/ldtDchromosome condensin MukBEF, ATPase and DNA‑binding subunit/murein L,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (9/20);  total (9/20)

TCGGCCTGCGAGGATTTGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTAAAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCGGCGTTTATATACTGAAGATAAGCCTGATGAGTAACAGGCTTGCTCGTCATA  >  NC_000913/980710‑980962
                                                                                                                                     |                                                                                                                       
tcgGCCTGCGAGGATTTGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTaaaaag                                                                                                                    >  1:1229019/1‑138 (MQ=255)
tcgGCCTGCGAGGATTTGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTaaaaag                                                                                                                    <  1:395644/139‑2 (MQ=255)
tcgGCCTGCGAGGATTTGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTaaaaag                                                                                                                    >  2:1102660/1‑138 (MQ=255)
                tGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACg                                                                                                       <  2:446010/135‑1 (MQ=255)
                tGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACg                                                                                                       >  1:446010/1‑135 (MQ=255)
                             ccTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTaaa                                                                                      <  2:766429/139‑1 (MQ=255)
                              cTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAAc                                                                                     <  2:764210/139‑1 (MQ=255)
                                  aaCGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAActtct                                                                                 <  2:589974/139‑1 (MQ=255)
                                  aaCGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAActtct                                                                                 <  1:224486/139‑1 (MQ=255)
                                  aaCGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAActtct                                                                                 <  2:1268649/139‑1 (MQ=255)
                                       ttCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACa                                                                            <  2:1329483/139‑1 (MQ=255)
                                        tCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCCTTTCTTTAAACTTCTTTACAt                                                                           <  1:1102660/139‑1 (MQ=255)
                                             gAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGt                                                                      <  2:1229019/139‑1 (MQ=255)
                                              aaCTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGtt                                                                     <  1:162528/139‑1 (MQ=255)
                                                             ttCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATc                                                      <  1:291610/139‑1 (MQ=255)
                                                               ctcAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCgg                                                    <  2:203287/139‑1 (MQ=255)
                                                                      gAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCgg                                                    >  2:517142/1‑132 (MQ=255)
                                                                      gAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCgg                                                    <  1:517142/132‑1 (MQ=255)
                                                                        gTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTaaaaag                                                                                                                    >  2:319396/1‑66 (MQ=255)
                                                                        gTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTaaaaag                                                                                                                    <  1:319396/67‑2 (MQ=255)
                                                                          tAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCGGCGTTTATATAc                                         >  1:738156/1‑139 (MQ=255)
                                                                                  aGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCGGCGTTtat                                             >  2:945582/1‑127 (MQ=255)
                                                                                  aGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCGGCGTTtat                                             <  1:945582/127‑1 (MQ=255)
                                                                                   ggcggcAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCt                                                                                                <  2:846705/75‑1 (MQ=255)
                                                                                   ggcggcAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCt                                                                                                >  1:846705/1‑75 (MQ=255)
                                                                                        cagcaATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATc                                                      <  2:183654/112‑1 (MQ=255)
                                                                                        cagcaATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATc                                                      >  1:183654/1‑112 (MQ=255)
                                                                                                   ccTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACa                                                                            <  2:931659/79‑1 (MQ=255)
                                                                                                   ccTTTTCTTTTTCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTGAAACTTCTTTACa                                                                            >  1:931659/1‑79 (MQ=255)
                                                                                                              tCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCt                                                                                                >  1:882713/1‑48 (MQ=255)
                                                                                                              tCCGAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCt                                                                                                <  2:882713/48‑1 (MQ=39)
                                                                                                                 gAAAACTCCGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCGGCGTTTATATACTGAAGATAAGCCTGATGAGTAACAGGCTTGCTCGTCATa  <  2:1197263/139‑1 (MQ=255)
                                                                                                                         cGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCgg                                                    >  2:1028514/1‑81 (MQ=255)
                                                                                                                         cGTTTCTGCACT‑AAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCgg                                                    <  1:1028514/81‑1 (MQ=255)
                                                                                                                                     |                                                                                                                       
TCGGCCTGCGAGGATTTGCGCCGCAACTCCCTGAAACGCTTCCAGGAACTGACGAAGCGCCTTCTCAGGCGAGTTAAAATTAAGGCGGCAGCAATGCCGCCTTTTCTTTTTCCGAAAACTCCGTTTCTGCACTAAAAAAGTGGCACATTACGGCGCGCTTTTCTTTAAACTTCTTTACATTAGGTTATGTAAAAACGTATCGGCGTTTATATACTGAAGATAAGCCTGATGAGTAACAGGCTTGCTCGTCATA  >  NC_000913/980710‑980962

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A