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
A1 F169 I0 R1 75 34.0 794130 95.7% 759982 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,186,228 T→C 34.9% T129T (ACA→ACG)  rsbW ← Serine‑protein kinase RsbW

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,186,2280TC34.9% 18.5 / 19.3 26T129T (ACA→ACG) rsbWSerine‑protein kinase RsbW
Reads supporting (aligned to +/- strand):  ref base T (12/5);  new base C (6/3);  total (18/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.93e-01

TGGTGTTCTTTAATCCATTGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTAT  >  USA300TCH1516_ALE/2186090‑2186361
                                                                                                                                           |                                                                                                                                     
gggTGTTCTTTAATCCATAGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTCTATACTTATGCATACTGCACGCAAGCCCACATTCGTTATATACtgt                                                                                                                                     >  2:5227/2‑141 (MQ=255)
            aTCCATTGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCAt                                                                                                                         <  1:380106/141‑1 (MQ=255)
                        aTTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCgtt                                                                                                             >  1:1410/1‑139 (MQ=255)
                        aTTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGAt                                                                                                             >  1:160491/1‑141 (MQ=255)
                             cTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTaaaa                                                                                                        >  1:262299/1‑141 (MQ=255)
                                       aTTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGCTTGCCTCACCATAGTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAg                                                                                              >  1:188555/1‑141 (MQ=255)
                                          ttcttAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACTCCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGcc                                                                                           <  2:208376/138‑1 (MQ=255)
                                           cATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGCTTAAAAATAAACCTAGGCCa                                                                                          >  1:46692/1‑141 (MQ=255)
                                                   gATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTcgcg                                                                                  <  2:224372/141‑1 (MQ=255)
                                                           ctctTTCGCCATTATTTCG‑ACTGGTCTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGt                                                                          >  1:392862/1‑141 (MQ=255)
                                                                       tattTCGCCCCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGt                                                              <  1:313100/141‑1 (MQ=255)
                                                                         tttCGCACCTG‑CTCTTATTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCt                                                            >  1:234584/1‑141 (MQ=255)
                                                                                       ctTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTTAGGAc                                               >  1:261565/1‑141 (MQ=255)
                                                                                          tttttATATACTTAATCATACTGATTATCACACCAGATTCTTTATACACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTa                                            <  2:233225/141‑1 (MQ=255)
                                                                                             ttATATACTTAGTCATACTGATTATCACACCAGATTCTTTATGTACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCCCCTTCGCCTCAAAACGCTATATTTTCGTCATTATCATTAGGACCTActt                                         >  2:225503/1‑141 (MQ=255)
                                                                                                tataCTTAATCATACTGCTTGTGTCACCTTAGTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTg                                      >  1:192016/1‑141 (MQ=255)
                                                                                                    cTTAGTCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTACGACCCTATTTTTGAttt                                  >  2:63502/1‑141 (MQ=255)
                                                                                                        gTCATACTGATTGTCACACCAGATTCTTTATATACTGTGAATTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATCTTTGATTCAgtt                              <  1:279566/141‑1 (MQ=255)
                                                                                                                gATTGTCATACCTGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATa                      <  2:308911/141‑1 (MQ=255)
                                                                                                                gATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATa                      <  2:314746/141‑1 (MQ=255)
                                                                                                                      cacaCCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCaaa                >  1:384905/1‑141 (MQ=255)
                                                                                                                          ccAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGAACCTATTTTTAATTTAGTTGTTTTCTAATCAAAAcgg            >  1:148363/1‑139 (MQ=255)
                                                                                                                          ccAGAAACTTTATATACTGTGACTTCATCACTTAGAGATTCGCTTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCATCTTCATCATCCGTACCTATTTTTGATTTAGTTGTTTCATAATCAGAACTg            >  2:140552/1‑141 (MQ=255)
                                                                                                                              aTTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCAc        >  2:70407/1‑141 (MQ=255)
                                                                                                                              aTTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCAc        >  2:87868/1‑141 (MQ=255)
                                                                                                                                    tatataCTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTAt  >  1:385164/1‑141 (MQ=255)
                                                                                                                                    tatataCTGTGACTTCATCCAGTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTAt  >  1:310214/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                     
TGGTGTTCTTTAATCCATTGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTAT  >  USA300TCH1516_ALE/2186090‑2186361

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