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
A19 F106 I1 R1 24 58.2 1363720 92.2% 1257349 135.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 39,378 C→A D586Y (GAT→TAT)  mecA ← penicillin binding protein 2 prime

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073039,3780CA100.0% 138.7 / NA 48D586Y (GAT→TAT) mecApenicillin binding protein 2 prime
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (24/24);  total (24/24)

ATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTTAATAAGTGAGGT  >  CP000730/39251‑39496
                                                                                                                               |                                                                                                                       
atcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTa                                                                                                                  <  2:124579/135‑1 (MQ=255)
   atGTTTGGATTATCTTTATTATATGATATAAACCACCCAATTTGTCTGTTAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTAtgt                                                                                                               <  1:265612/135‑1 (MQ=255)
   atGTTTGGATTATCTTTATCATATGATATAAACCACCCGATTTGTCTGCCTGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTAtgt                                                                                                               <  1:265664/135‑1 (MQ=255)
        tGGATTATCTTTATCTTATGATATTAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGCGTTCTGTAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGtttt                                                                                                          <  2:476705/135‑1 (MQ=255)
            ttATCTTTATCATATGATATAAACCACCCAATTTGTCTGCACGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttattt                                                                                                      >  2:154988/1‑135 (MQ=255)
                 tttATCATTTGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGAc                                                                                                 <  2:188019/135‑1 (MQ=255)
                 tttATCATATGATATAACCCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGAc                                                                                                 <  2:111603/135‑1 (MQ=255)
                 tttATCATATGATATAAACCACCCAATTTGTCTGTCAGGTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGAc                                                                                                 <  1:103839/135‑1 (MQ=255)
                       atatGATATAAACCACCCTATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACttgttg                                                                                           <  1:253246/135‑1 (MQ=255)
                        tatGATATAAACCACCCCATTTGTCTGCCAGCTCCTCCCTGCTTTGTTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGc                                                                                          <  1:291882/135‑1 (MQ=255)
                         atGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCa                                                                                         <  2:511995/135‑1 (MQ=255)
                         atGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCa                                                                                         <  2:513874/135‑1 (MQ=255)
                               taAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCAt                                                                                   >  2:35400/1‑135 (MQ=255)
                               taAACCACCCAATTTGTCTGCAAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCAt                                                                                   >  1:366455/1‑135 (MQ=255)
                                aaaCAACCAAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTACAGTAACGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATCCCATc                                                                                  >  2:139525/1‑135 (MQ=255)
                                   ccaccCAATTTGTCTGCCAGTTACTCCTTGTTTCATTTTAAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGt                                                                               >  1:107373/1‑135 (MQ=255)
                                   ccaccCAATTTGTATGCCAGATTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTATGACTTGTTGCATACCATCAGt                                                                               >  1:544224/1‑135 (MQ=255)
                                      cccAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTaa                                                                            >  1:561833/1‑135 (MQ=255)
                                      cccAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATATGTTTTATTTAGGACTTGTTGCCTACCATCAGGTaa                                                                            >  1:245043/1‑135 (MQ=255)
                                            ttGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTGTTTGCATGCCATGAGTTCAtgggtt                                                                      >  2:409027/1‑130 (MQ=255)
                                              gTCTGCTAGTTTTTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGa                                                                    <  1:56343/135‑1 (MQ=255)
                                              gTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATTTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGa                                                                    <  1:246570/135‑1 (MQ=255)
                                                  gccagggtgtcattGTTTCATTTTGAGTTCTGCAGTACCGGCTTTGCCAATTAAGTTTGCATAAGATCTATAAATATATGCTTGATGTGTTTAATTTACGACTTGTTGCATACCATCCGTTATTAAATTGATAtt                                                                >  2:150964/13‑135 (MQ=255)
                                                  gCCTGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                >  1:365376/1‑135 (MQ=255)
                                                  gCCCGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                >  1:156906/1‑135 (MQ=255)
                                                  gCCCGTTTCTCCTTGTTTCATATAGAGTTCTGCAGTACCGAATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTTTTGCATACCATCAGTTAATAGATTGATAtt                                                                >  1:76573/1‑135 (MQ=255)
                                                  gCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                <  2:34119/135‑1 (MQ=255)
                                                  gCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATATACGACTTGTTGCATACCATCAGTTAATAGATTGATAtt                                                                <  2:298184/135‑1 (MQ=255)
                                                   ccAGTTTCTCCTTGTTTCATTTTGAGATATGCAGTACCGGATTTGCCAATTAAGTTTGCATGAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAttt                                                               >  1:189328/1‑135 (MQ=255)
                                                         tctcCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTg                                                         <  2:296832/135‑1 (MQ=255)
                                                         tctcCCTGTTTCATTTTGAGTTCTGCAGTATCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTg                                                         <  2:118626/135‑1 (MQ=255)
                                                         tctcCCTGTATCATTTTCAGTTCTTCATTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTg                                                         <  2:262753/135‑1 (MQ=255)
                                                            ccTTGTTTCTTTTTGAGTTATGCAGTAACGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCATTTAATAGATTGATATTTTCTTTTGaa                                                      >  1:588385/1‑135 (MQ=255)
                                                               tGTTTCATTTTGAGTTCTGCAATACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaata                                                   >  1:212509/1‑135 (MQ=255)
                                                                        ttGAGTTCTGCAGTACCGGATTTGCCAATAAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttc                                          >  1:30298/1‑135 (MQ=255)
                                                                         tgtgTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttct                                         >  1:574368/4‑135 (MQ=255)
                                                                                 gCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGTTATTTTTTTTGGAAATAATATTTTTCTTCCAAACt                                 <  1:572452/135‑1 (MQ=255)
                                                                                 gCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATCTTTTCTTTGGAAATCATATTTTTCTTCCaaaat                                 >  1:70428/1‑133 (MQ=255)
                                                                                  cAGTACCGGATTTGCCAATTAAGTTTGCATAATATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACtt                                <  2:57900/135‑1 (MQ=255)
                                                                                   aggaCCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACttt                               <  2:515469/132‑1 (MQ=255)
                                                                                    gTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACAATCAGTTAATTGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTg                              >  2:251381/1‑135 (MQ=255)
                                                                                       ccGGATTTGTCAATTAAGTTTGCATAAGATTTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGttt                           <  2:489872/135‑1 (MQ=255)
                                                                                           aTTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCg                       >  1:496492/1‑135 (MQ=255)
                                                                                           aTTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTATTATTTACGACTTTGTGGATAACATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTGTTGTTCAAAACTTGGTTATTCg                       >  2:266838/1‑135 (MQ=255)
                                                                                                     tAAGTTTGCATATGATCTATAAATATATTCTTTATTTGTTTTATTTACGACTTGTTGCATACCATCTGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTtaa            <  2:494222/135‑1 (MQ=255)
                                                                                                     tAAGATTGCATAAGATCTATAAATATATTCGGGATGTGTTGTATTTACGACGTGTTGCATACCATCTGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCGAAACTTTGTTTTTCGTG‑TCTTTtaa            >  2:272679/1‑135 (MQ=255)
                                                                                                               tAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTT‑GTGTTCTTTTAATTAGTGATGt  >  2:483811/1‑135 (MQ=255)
                                                                                                               tAAAATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTTAATAAGTGAggc  <  1:150964/135‑2 (MQ=255)
                                                                                                                               |                                                                                                                       
ATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTG‑TCTTTTAATAAGTGAGGT  >  CP000730/39251‑39496

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