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
A21 F21 I0 R1 92 47.7 1834152 89.2% 1636063 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 595,519 T→A 23.8% intergenic (‑76/‑81) cusR ← / → cusC DNA‑binding transcriptional activator CusR/copper/silver export system outer membrane channel

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913595,5190TA23.8% 56.7 / 16.2 37intergenic (‑76/‑81)cusR/cusCDNA‑binding transcriptional activator CusR/copper/silver export system outer membrane channel
Reads supporting (aligned to +/- strand):  ref base T (13/15);  new base A (6/3);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.85e-01

TTCGGTTAACCCTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACT  >  NC_000913/595378‑595658
                                                                                                                                             |                                                                                                                                           
ttCGGTTAACCCTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGGTCAGATGGCAATCGCTTATTGGCCAAATGACAAtt                                                                                                                                            >  1:242337/1‑143 (MQ=255)
  cGGTTAACCTTTTGGTCGAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAGCAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAtttt                                                                                                                                          <  2:468311/143‑1 (MQ=255)
  cGGTTAACCCTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCCTATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAtttt                                                                                                                                          <  2:739376/143‑1 (MQ=255)
   ggTTAACCCTTTGATCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACACTCAACAGTTTCATCTTTCCTCCGCCTGTTGCCCCGGCCATTCTCGAGTAGACGTATCAGATGGCAATCCCGCATTAGCAAAATGCCAAttacg                                                                                                                                         >  2:802507/1‑140 (MQ=255)
     ttAACCCTTTGGTCACGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGATTCATATTTCATCAGCATATTGCTCGACCTATTCTAGAACAGCGAGCTCATGTGGCAAGCGCATAGTGGCGGAATGACAAATTTGtg                                                                                                                                       >  2:789585/1‑142 (MQ=255)
          ccTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATGAACAGTGTCCAAAATCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAAATTGTCAtttt                                                                                                                                  <  1:417869/143‑1 (MQ=255)
          ccTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAAATTGTCAtttt                                                                                                                                  <  2:151701/143‑1 (MQ=255)
           cTTTTGTCAAGTATTCTCCCGTTTTCCTCTCATCTCCGACAATCAACAGTTTCATATTTCCCCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAAATTGTCAttttg                                                                                                                                 <  1:259041/143‑2 (MQ=255)
           cTTTAGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCAttttt                                                                                                                                 <  2:318502/143‑1 (MQ=255)
                 tCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTGTTCTGTCa                                                                                                                           >  1:321238/1‑143 (MQ=255)
                        ttCTCCGGTTTTCTTGTCATCTGCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGaaa                                                                                                                    <  2:660671/143‑1 (MQ=255)
                           tcCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGCTCAGATGGCAACCGCTTCTTGGCAAAATGGCAATTTTGTCATTTTTCTGTTACCGGGAAGTc                                                                                                                 >  2:383022/1‑143 (MQ=255)
                            cctgTTTGCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCa                                                                                                                <  1:358871/140‑1 (MQ=255)
                              ggTTGTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCaga                                                                                                              <  1:223365/143‑1 (MQ=255)
                               gTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGGAGCGGCACCAGCTGGCATGCTCTTAGTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCagag                                                                                                             <  1:621901/143‑1 (MQ=255)
                                       ttcATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAACATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGa                                                                                                     >  1:322960/1‑143 (MQ=255)
                                           tCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCCATCGCCTATTGGCAAAATGACAATTTTGTCATTTTTCTATCACCGGAAAATCAGAGCCTGGCGAGtca                                                                                                 >  2:123969/1‑141 (MQ=255)
                                            cTTCGACAATCAACTGTTTCATATTCCCTACGCATGTTGTACGTGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTaaa                                                                                                <  2:400025/143‑1 (MQ=255)
                                             ttCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACCATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAg                                                                                               >  1:166644/1‑143 (MQ=255)
                                                  cAAGCAACAGTTGCATATTGCCTCCGCATGTTGCCCGGGCAATGCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTggc                                                                                          <  1:441031/143‑1 (MQ=255)
                                                                  atTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAAGCACCAg                                                                          >  1:790768/1‑143 (MQ=255)
                                                                        tccGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAAATGTGTCATTTTTCTGTCCCCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCAACAGAAAtac                                                                    >  2:718606/1‑141 (MQ=255)
                                                                         ccGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTAGCGGCATAAAATCACCAGAAATTAt                                                                   >  1:354518/1‑143 (MQ=255)
                                                                            cATGGTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAg                                                                <  1:136538/143‑1 (MQ=255)
                                                                                       ggCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGGAATTATGAGCCTATGTCTcc                                                     >  1:450075/1‑143 (MQ=255)
                                                                                             tcgagagTAGCGGGTTCAGACGGCAAATGTTTATTGGCAAAGAATAAATTTTGTCATTTTTCTGTCACCTGCAAATGAGAGCGTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTaa                                               <  2:787160/140‑1 (MQ=255)
                                                                                             tCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTaa                                               <  1:638982/143‑1 (MQ=255)
                                                                                               tAGAGTAGCGGGAGCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAAc                                             <  1:66082/143‑1 (MQ=255)
                                                                                                          gATCAGATGGCAATCGCTTATTGGCAACACGACAATTAAGTCATGTGTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGACTATGTCTCCTTGTCAACGTCTGCCActt                                  >  1:172836/1‑143 (MQ=255)
                                                                                                               gATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGACACTAACCATTGATTTTGGCGGTATTAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTtgtgt                             <  1:668481/143‑1 (MQ=255)
                                                                                                                aTGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTtgtgtg                            >  1:121782/1‑143 (MQ=255)
                                                                                                                   gCAACCGCTTATCGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGcc                         <  2:696250/143‑1 (MQ=255)
                                                                                                                         gCTTAGTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTgcg                   <  1:804800/143‑1 (MQ=255)
                                                                                                                                agaaaaaTGACAAAATTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAACGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCg            >  2:450381/4‑143 (MQ=255)
                                                                                                                                agaaaaaTGACAAAATTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCCTGCGCTAACCg            >  2:183607/4‑143 (MQ=255)
                                                                                                                                agaaaaaTGACAAAATTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGGAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCg            >  1:522744/4‑143 (MQ=255)
                                                                                                                                   aaaaTGATAATTTTTTCATTTTTCTGTCACAGTAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGgtt         <  1:38676/143‑1 (MQ=255)
                                                                                                                                   aaaaTGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTACACTTCTGCCATTTTGTGTGGCCCTTGCCCTAACCggct         >  2:631447/1‑141 (MQ=255)
                                                                                                                                    aaaTGGCAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGgttg        >  1:585233/1‑143 (MQ=255)
                                                                                                                                      aTGACAAAATTGTCATTTTTCTGTCACCGTAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTCTGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCCCTAACCGgttgtt      >  2:555375/1‑143 (MQ=255)
                                                                                                                                          cAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACt  >  1:135460/1‑143 (MQ=255)
                                                                                                                                             |                                                                                                                                           
TTCGGTTAACCCTTTGGTCAAGTATTCTCCGGTTTTCTTTTCATCTTCGACAATCAACAGTTTCATATTTCCTCCGCATGTTGCCCGGGCAATTCTAGAGTAGCGGGATCAGATGGCAATCGCTTATTGGCAAAATGACAATTTTGTCATTTTTCTGTCACCGGAAAATCAGAGCCTGGCGAGTAAAGTTGGCGGCATAAAATCACCAGAAATTATGAGCCTATGTCTCCTTGTAAACTTCTGCCATTTTGTGTGGCCCTTGCGCTAACCGGTTGTTCACT  >  NC_000913/595378‑595658

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