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
A5 F28 I1 R1 260 73.5 2514320 99.3% 2496719 138.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,637,743 (A)9→8 coding (1048/1425 nt) creC → sensory histidine kinase CreC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,637,7350A.95.0% 149.3 / 3.2 40coding (1040/1425 nt)creCsensory histidine kinase CreC
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base . (23/15);  total (24/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

CGCGTATGCAGGCATTGGTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAG  >  NC_000913/4637600‑4637870
                                                                                                                                       |                                                                                                                                       
cgcgTATGCAGGCATTGGTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGaaaaa                                                                                                                                     >  1:2816/1‑140 (MQ=255)
        cAGGCATTGGTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCAct                                                                                                                            <  2:185468/140‑1 (MQ=255)
        cAGGCATTGGTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCAct                                                                                                                            <  1:1141842/140‑1 (MQ=255)
                ggTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGt                                                                                                                    >  2:1032006/1‑140 (MQ=255)
                 gTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGtt                                                                                                                   >  1:744578/1‑140 (MQ=255)
                     aaaCGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGc                                                                                                               >  2:66640/1‑140 (MQ=255)
                          ttACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCAcc                                                                                                          <  1:896142/140‑1 (MQ=255)
                                cGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGtt                                                                                                    <  2:744578/140‑1 (MQ=255)
                                  ccAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTaa                                                                                                  <  1:1032006/140‑1 (MQ=255)
                                   cAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAAc                                                                                                 >  2:805337/1‑140 (MQ=255)
                                    aGGCAAGACTGGAGAATCGCCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGCTGGCAG‑GAAAAAAATCACTCTGCATGTTACGCCCACCGAGGCTAACg                                                                                                >  2:755575/1‑140 (MQ=255)
                                       cAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTtg                                                                                             >  2:273684/1‑140 (MQ=255)
                                          gACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTtgctg                                                                                          >  2:190040/1‑140 (MQ=255)
                                           aCTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTtgctgc                                                                                         >  2:1144977/1‑140 (MQ=255)
                                               gagaATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGaa                                                                                     >  2:1072970/1‑140 (MQ=255)
                                                agaATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAAc                                                                                    <  2:2816/140‑1 (MQ=255)
                                                   aTCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCgg                                                                                 <  2:509140/140‑1 (MQ=255)
                                                   aTCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCgg                                                                                 <  2:270733/140‑1 (MQ=255)
                                                    tCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCg                                                                                  <  1:18824/138‑1 (MQ=255)
                                                    tCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCg                                                                                  >  2:18824/1‑138 (MQ=255)
                                                                 gTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAg                                                                   >  2:806750/1‑140 (MQ=255)
                                                                  ttCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAgg                                                                  >  2:92892/1‑140 (MQ=255)
                                                                  ttCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAgg                                                                  >  2:750786/1‑140 (MQ=255)
                                                                       gctgctgTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTg                                                             <  1:755575/139‑1 (MQ=255)
                                                                           ctgTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGaa                                                         <  2:1197111/140‑1 (MQ=255)
                                                                                        ggcATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATa                                             >  1:362820/1‑140 (MQ=255)
                                                                                        ggcATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATaa                                            >  1:691160/1‑140 (MQ=255)
                                                                                           attattCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGc                                         >  2:964955/1‑140 (MQ=255)
                                                                                                     cgcgTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGACAACGCCATCGAtttt                               <  1:266042/140‑1 (MQ=255)
                                                                                                       cgTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTa                              <  2:362820/140‑1 (MQ=255)
                                                                                                       cgTCAGCGAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTAc                             >  1:906726/1‑140 (MQ=255)
                                                                                                              gAAGCGCGCACCGTGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCgag                      <  1:144543/140‑1 (MQ=255)
                                                                                                                           tGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCa         >  2:476747/1‑140 (MQ=255)
                                                                                                                           tGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCa         >  1:994672/1‑140 (MQ=255)
                                                                                                                           tGCAGTTGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCa         >  1:1101445/1‑140 (MQ=255)
                                                                                                                                 tGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGc             >  2:35203/1‑130 (MQ=255)
                                                                                                                                 tGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGc             <  1:35203/130‑1 (MQ=255)
                                                                                                                                 tGGCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTaa   >  2:551107/1‑140 (MQ=255)
                                                                                                                                  ggCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAg  <  1:805337/140‑1 (MQ=255)
                                                                                                                                  ggCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAg  >  1:602903/1‑140 (MQ=255)
                                                                                                                                  ggCAG‑AAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACACCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAg  >  2:633067/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CGCGTATGCAGGCATTGGTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAG  >  NC_000913/4637600‑4637870

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A