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 F184 I0 R1 46 69.8 1527574 94.8% 1448140 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,233,504 T→A 100% V470D (GTT→GAT)  USA300HOU_1157 → non‑specific serine/threonine protein kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,233,5040TA100.0% 159.1 / ‑6.5 52V470D (GTT→GAT) USA300HOU_1157non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base A (25/26);  total (26/26)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGTT  >  CP000730/1233369‑1233637
                                                                                                                                       |                                                                                                                                     
gTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACg                                                                                                                                   >  2:312087/1‑140 (MQ=255)
  gAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTTTTAAAGATGATACGAt                                                                                                                                 <  1:422117/140‑1 (MQ=255)
   aaCGTGTTGAACGTGGTGACAGTGTTTATGTTGTTATATCAACGGTACCCTAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAtt                                                                                                                                <  1:358381/140‑1 (MQ=255)
   aaCGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAtt                                                                                                                                >  1:408963/1‑140 (MQ=255)
   aaCGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAtt                                                                                                                                <  1:488350/140‑1 (MQ=255)
    aCGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAACGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTg                                                                                                                               <  2:386018/140‑1 (MQ=255)
        gtTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaaaa                                                                                                                           >  1:636360/1‑140 (MQ=255)
               gtggtgACAGCGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAACATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGtatat                                                                                                                    <  1:589554/140‑1 (MQ=255)
                  gtgACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTTGGTCTTAAAGATGATACGATTGAACAAGTATataat                                                                                                                 >  1:185399/1‑140 (MQ=255)
                  gtgACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATataat                                                                                                                 <  2:286317/140‑1 (MQ=255)
                  gtgACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATataat                                                                                                                 >  1:383960/1‑140 (MQ=255)
                  gtgACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATataat                                                                                                                 <  2:726838/140‑1 (MQ=255)
                  gtgACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATataat                                                                                                                 >  2:508208/1‑140 (MQ=255)
                  gtgACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGAATataat                                                                                                                 >  1:564509/1‑140 (MQ=255)
                    gataGTGTTAAAGTAGATATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGAAAAAAAAAAAAAAAAAGTATAtaataa                                                                                                               <  2:714739/137‑1 (MQ=255)
                        tgtttGATGTTGTTAGAGCAAAGGGCCCGGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCaa                                                                                                           <  2:303848/137‑1 (MQ=255)
                        gaaataaagtagaaataaCAAAGGGACAAGAAAAGGTTAAAATGACAAATGACAGTGGTTTACCTAAGGAGGAAGCCATACAGAAATTAAAATCGTTATGTCTTAAAGAAAAAAAAAAAAAAAAAGTATATAATAATCaa                                                                                                           <  2:332021/126‑1 (MQ=255)
                                    ttATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAGTCAAGCGCCAAAAGGa                                                                                               <  1:452654/140‑1 (MQ=255)
                                       tatCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATAc                                                                                            >  2:388881/1‑140 (MQ=255)
                                             aGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCa                                                                                      >  1:109190/1‑140 (MQ=255)
                                             aGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCa                                                                                      >  1:109410/1‑140 (MQ=255)
                                               ggCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCaaa                                                                                    >  1:354815/1‑140 (MQ=255)
                                                 ccatGAAAAGGTTAAAATGCCAAATGACAATGGTTAAACTAAAGAGGACGCAAAGCAGAAATTAAAAACGTTAGGACTCAAAGATGATAAGAATGAAGACGTATATAATAATCAAACGACAAAAGGATAAAATGCAAAta                                                                                  >  2:589595/4‑139 (MQ=255)
                                                  ccTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCATTGCAGAACTTAATATCGTTTGGTCTTAAAGATGTGACGATAGAAAAAGAATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCa                                                                                 >  2:751691/1‑140 (MQ=255)
                                                     gAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAg                                                                              >  1:42352/1‑140 (MQ=255)
                                                         aGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTa                                                                          >  1:105810/1‑140 (MQ=255)
                                                             tAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGAATAGATTGCAAATCAAAATGTAACCg                                                                      >  1:77260/1‑140 (MQ=255)
                                                                 aTGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAATCTCCAAAAAGATTCATAGCAAATCAAAGTGTAACCGCaaa                                                                  >  1:343832/1‑140 (MQ=255)
                                                                  tGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGGTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACAGCAAAt                                                                 >  2:211668/1‑140 (MQ=255)
                                                                    ccAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATAc                                                               <  2:408963/140‑1 (MQ=255)
                                                                         tGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCATTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCAAAAAGGATACATTGCAAAACAAAGTATAACCACAAATACTGaaa                                                          >  1:651500/1‑140 (MQ=255)
                                                                             aTTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATGGc                                                      >  2:399225/1‑140 (MQ=255)
                                                                                  tttATCTAAAGACGTAGCCTTGCAGAAATTAAAATCGTTACGTCTTAAAGATCATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAATGATACATTCCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTc                                                 <  2:260918/140‑1 (MQ=255)
                                                                                  tttACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCACAGTGTAACCGCAAATACTGAAATCGCTAGTc                                                 <  2:444658/140‑1 (MQ=255)
                                                                                      ccTAATGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGa                                             <  1:662608/140‑1 (MQ=255)
                                                                                         aaGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTc                                          >  1:641346/1‑140 (MQ=255)
                                                                                          aggaggAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCt                                         >  2:121946/1‑140 (MQ=255)
                                                                                           ggaggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTa                                        <  2:749128/140‑1 (MQ=255)
                                                                                           cgaggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTa                                        <  1:448685/139‑1 (MQ=255)
                                                                                                aaGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATAtt                                   <  1:312087/140‑1 (MQ=255)
                                                                                                    cTTGCAGAAATTAAAATTGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAAc                               <  1:444584/140‑1 (MQ=255)
                                                                                                     ttGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGAAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTGTTGATTTTAATGTTGAACt                              >  2:309890/1‑140 (MQ=255)
                                                                                                         aGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTatat                          <  1:448664/140‑1 (MQ=255)
                                                                                                          gAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATg                         >  1:282029/1‑140 (MQ=255)
                                                                                                          gAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATg                         >  1:722086/1‑140 (MQ=255)
                                                                                                                   aTCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAg                <  1:679050/140‑1 (MQ=255)
                                                                                                                      gTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCa             <  2:84734/140‑1 (MQ=255)
                                                                                                                      gTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCa             >  1:614469/1‑140 (MQ=255)
                                                                                                                      gTTAGGTCCTAAACATGAAACCAATGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACACCAACTACTCAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTCTAGGCa             <  2:346624/140‑1 (MQ=255)
                                                                                                                         aGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAATTATATGAATCTTTAGGCATTa          <  1:388881/140‑1 (MQ=255)
                                                                                                                               tAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAg    <  1:339740/140‑1 (MQ=255)
                                                                                                                                 aaGATGATACGATTCAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGtt  <  2:354815/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                     
GTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGTT  >  CP000730/1233369‑1233637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A