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
A13 F191 I0 R1 47 68.0 1456600 97.2% 1415815 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 423,247 A→G 100% V112V (GTA→GTG)  USA300HOU_0394 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730423,2470AG100.0% 140.8 / ‑6.5 50V112V (GTA→GTG) USA300HOU_0394hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (20/29);  minor base T (0/1);  total (20/30)
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.

TTTTTAATAAAGAAGGGAAAGAGACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTACCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTGTAATAATTATGAATAAAATT  >  CP000730/423114‑423381
                                                                                                                                     |                                                                                                                                      
tttaatatagAGAAGGGAAAGAGAGTCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATACATACTTCAAAATTACACATAACGGTCATCATGTAGAAACTTATGAAAAAATTAAAAAGGAAGAAGTGCCaaag                                                                                                                                  <  2:617310/134‑1 (MQ=255)
    taataaAGAAGGGAAAGAGACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTAAACATACAGGTCATCATGTAGAAACTTTTGAAGAAGTGGAAAAGTAAGAAGTGCCaaagaaag                                                                                                                              >  2:659278/1‑140 (MQ=255)
      ataaAGAAGGGAAAGAGACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCa                                                                                                                            >  1:221858/1‑140 (MQ=255)
         aagaagGGAAAGAGACGCAATTAATGTATACTGCTAAATTTGATGGTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGATGAAAAGGAAGAAGTGCCAAAGAAAGAAtag                                                                                                                         >  2:678355/1‑138 (MQ=255)
            aagGGAAAGAGACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAACATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGAATTAGAc                                                                                                                      >  1:144907/1‑140 (MQ=255)
                  aaGAGACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCCACGAAAGCAATAGACAACCTg                                                                                                                >  2:209756/1‑140 (MQ=255)
                   agagACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGTAGGAGTGCCAAAGAAAGCATTAGACAAACTGa                                                                                                               >  2:407268/1‑140 (MQ=255)
                    gagaCGAAATTAATGTACACTGCTACATTAGATGTTAAACCGCATAGATACTTTAAAAATAAACATAACGGCCACCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACaaaatata                                                                                                              <  2:186683/140‑6 (MQ=255)
                    gacaCGCAATTAATGTATACTGTTACATTTGATGTTAAACCGAATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAg                                                                                                              <  1:28610/137‑1 (MQ=255)
                      gaCGCAATTAATGTAAACTGCTACATTTGATGATAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTTCCAAAGAAAGCATTAGACAAACTGAGTc                                                                                                            <  2:412683/140‑1 (MQ=255)
                         gCAATTAATGTATACTGCTACATTTGTTGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGat                                                                                                         <  1:558529/140‑1 (MQ=255)
                         gCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGat                                                                                                         >  1:460487/1‑140 (MQ=255)
                         gCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGat                                                                                                         <  1:606248/140‑1 (MQ=255)
                          cAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGata                                                                                                        >  2:292488/1‑140 (MQ=255)
                                   tataCTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGc                                                                                               >  1:451101/1‑140 (MQ=255)
                                      aCTGCTACATTTGATGTTAACCCGCAAAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTta                                                                                            <  2:377310/140‑1 (MQ=255)
                                             cATTTGCTGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGCAGAAGTGCCAAAGCAACCATTAGACAAACAGATCCGGTAACACCACGCttacattaca                                                                                     >  2:499605/1‑140 (MQ=255)
                                               tttGATGTTTATCTGTATAGATACTTGAAAATTCCACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATg                                                                                   <  1:673421/140‑1 (MQ=255)
                                                      ttAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCAtt                                                                            >  1:77277/1‑140 (MQ=255)
                                                            cGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATaaa                                                                      >  2:136224/1‑140 (MQ=255)
                                                              cATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAg                                                                    <  2:460487/140‑1 (MQ=255)
                                                                   aTACTTGAAAATTACACATAAAGGTTATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTa                                                               <  1:283644/140‑1 (MQ=255)
                                                                   aTACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGACGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGGCGATAATAGCTTGCTTATATTACATGGTTCATTTATAAAAGGAGTa                                                               <  1:386940/140‑1 (MQ=255)
                                                                   aTACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATTGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTa                                                               <  1:717244/140‑1 (MQ=255)
                                                                    taattGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTac                                                              >  2:12876/4‑140 (MQ=255)
                                                                         gAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTacgaacg                                                         <  2:524293/140‑1 (MQ=255)
                                                                         gAAAAATACACATAAAGGTAATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTacgaacg                                                         <  2:524269/140‑1 (MQ=255)
                                                                          aaaaacacacAGAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTacgaacga                                                        <  2:176881/134‑1 (MQ=255)
                                                                              ttACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGt                                                    <  2:381406/140‑1 (MQ=255)
                                                                              ttACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGt                                                    <  2:550947/140‑1 (MQ=255)
                                                                              ttACAAATAAAGGTCATCATGTAAAAACTTTAGAAGAAGTTAAAAAGTAAGAAGTGCCAAAGAAAGTATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGTAGTACGAACGAAAGt                                                    <  2:458959/140‑1 (MQ=255)
                                                                                  acaTAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGCAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACg                                                >  1:628040/1‑140 (MQ=255)
                                                                                     tAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCAt                                             <  1:519152/140‑1 (MQ=255)
                                                                                           tcatctTGTAGAAACTTTTGNANAAGNTGAAAAGGAAGAAGTGCCAAAGAACGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATgatgat                                       <  1:522412/140‑1 (MQ=255)
                                                                                           tcatcaTGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGAt                                       >  1:160029/1‑140 (MQ=255)
                                                                                           tcatcaTGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCAAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTGATTTATAAAAGGAGTAAGAACGAAAGTAACGCATGACGAt                                       >  2:588599/1‑140 (MQ=255)
                                                                                            catcatGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGAtt                                      >  1:263429/1‑140 (MQ=255)
                                                                                              tcatGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTaa                                    <  1:70664/140‑1 (MQ=255)
                                                                                                atGTAGAAAGTTTTGAAGAAGTTGAAAAGGAAGAAGGGCCAAAGAAAGCAGTAGACAACCTGAGTCGATAATAGCATGCTTGTATTACATGGTTCATTGTTAAAAGGAGTAGTAAGGAAAGGAATGCATGACGGTTAAtt                                  >  2:104167/1‑140 (MQ=255)
                                                                                                  gTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGATAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTa                                <  1:185823/140‑1 (MQ=255)
                                                                                                  gTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAACGTAACGCATGACGATTAATTTa                                >  2:102111/1‑140 (MQ=255)
                                                                                                  gTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTa                                <  1:516345/140‑1 (MQ=255)
                                                                                                      aaaaTTGTGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTaaaaa                            <  2:427222/140‑1 (MQ=255)
                                                                                                            ttGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTg                      >  2:257887/1‑140 (MQ=255)
                                                                                                            ttGAAGAAGTTGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTg                      <  2:611136/140‑1 (MQ=255)
                                                                                                                     ttGAAAAGGAAGAAGTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTGTAATAATTa             <  1:3835/140‑1 (MQ=255)
                                                                                                                     gtGAAAAGGAAGAAGTGCCAAACAAAGCATTAGACAAACTGAGTCGATAATAGCAGGCGTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTGTAATAATTa             <  2:144907/139‑1 (MQ=255)
                                                                                                                        aaaaGGAAGAAGTGTCAAAGAAAGCTATAGACACACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAATGAGTACGAACGAACGTAACGCATGACGATTAATTTAATAATATTTGTAATAATTATGa          <  1:441422/140‑1 (MQ=255)
                                                                                                                               agaagGGCCAAAAAAATCATTAGACAAATTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTGTAATAATTATGAATAAAAt   <  1:27348/140‑1 (MQ=255)
                                                                                                                                taagTGCCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGCAACGCATGACGATTAATTTAAAAATATTTGTAATAATTATGAATAAAAtt  <  2:459889/139‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                      
TTTTTAATAAAGAAGGGAAAGAGACGCAATTAATGTATACTGCTACATTTGATGTTAAACCGCATAGATACTTGAAAATTACACATAAAGGTCATCATGTAGAAACTTTTGAAGAAGTTGAAAAGGAAGAAGTACCAAAGAAAGCATTAGACAAACTGAGTCGATAATAGCATGCTTATATTACATGGTTCATTTATAAAAGGAGTACGAACGAAAGTAACGCATGACGATTAATTTAAAAATATTTGTAATAATTATGAATAAAATT  >  CP000730/423114‑423381

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A