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 F121 I0 R1 43 32.8 695000 96.9% 673455 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 39,246 C→T 50.0% A630T (GCT→ACT)  mecA ← penicillin binding protein 2 prime

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073039,2460CT50.0% ‑5.8 / 20.6 18A630T (GCT→ACT) mecApenicillin binding protein 2 prime
Reads supporting (aligned to +/- strand):  ref base C (2/7);  new base T (5/4);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 3.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

GATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTA  >  CP000730/39109‑39385
                                                                                                                                          |                                                                                                                                           
gATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTATTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCcat                                                                                                                                          >  1:221019/1‑141 (MQ=255)
                                cGTAGTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGata                                                                                                          <  2:264900/141‑1 (MQ=255)
                                              cggTTCTCAGATATCTTATCATACACTTTACCTGAGATCTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTACTAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAAtt                                                                                            <  2:16905/139‑1 (MQ=255)
                                                    tcATATAGCTCATCCTACCCTTTACCTGAGATTTTGGCTTCGCAGGCTTCTTGTTCTTT‑ATCGTGTACATCATTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTg                                                                                      <  1:161777/141‑1 (MQ=255)
                                                                tcatACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGACTATCTTTATCGTATGATATAAACCACCCAATTTGTCGACCAGTTtctcat                                                                          >  2:236429/1‑139 (MQ=255)
                                                                  ctACACTTTTCCTGAGATTTTGGCATTGTAGCTAGCCATAACTTTAATCCACAACCT‑TTAATGACTAATAGTCATCATTATGTTTCTAGTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTg                                                                        <  2:332277/140‑1 (MQ=255)
                                                                    acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGtt                                                                      <  1:189813/141‑1 (MQ=255)
                                                                    acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGtt                                                                      <  1:255979/141‑1 (MQ=255)
                                                                               gagaTTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGt                                                           >  2:117440/1‑141 (MQ=255)
                                                                                                    gcCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGAGTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCa                                      >  1:229218/1‑141 (MQ=255)
                                                                                                      cATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAt                                    <  1:117440/141‑1 (MQ=255)
                                                                                                      cATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAt                                    <  2:26007/141‑1 (MQ=255)
                                                                                                        ttCTTTT‑ACCTTGTACATCTTCAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTa                                  <  1:91423/141‑1 (MQ=255)
                                                                                                                 tCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCa                          >  2:293478/1‑141 (MQ=255)
                                                                                                                 tCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCa                          <  2:339303/141‑1 (MQ=255)
                                                                                                                                     aaTAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAtcttc      >  2:283892/1‑141 (MQ=255)
                                                                                                                                      aTAGCGATCATCATGTTTGGATTATCCTTATCATATGATATAAACCTCCCCATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCACTAACGGATTTTCCAATTAAGTTTGCATAAGATCTATAAATAtattct     <  2:226490/141‑1 (MQ=255)
                                                                                                                                         gCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTa  >  1:104871/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                           
GATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTT‑ATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTA  >  CP000730/39109‑39385

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