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
A4 F1 I1 R1 73 24.7 1166784 93.9% 1095610 107.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,073,151 T→C L538P (CTG→CCG)  flu → CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,073,1510TC100.0% 82.4 / NA 23L538P (CTG→CCG) fluCP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/12);  total (11/12)

CTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGA  >  NC_000913/2073036‑2073265
                                                                                                                   |                                                                                                                  
ctcactGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGc                                                                                             >  2:285378/1‑139 (MQ=255)
    ctGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGaa                                                                                         <  1:285378/139‑1 (MQ=255)
             acacCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCac                                                                                >  1:243710/1‑138 (MQ=255)
               accacACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTg                                                                              >  1:140676/1‑139 (MQ=255)
                             gAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTg                                                                                                             >  2:541447/1‑94 (MQ=255)
                             gAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTg                                                                                                             <  1:541447/94‑1 (MQ=255)
                             gAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGCCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACtgtg                                                                                              <  2:49309/109‑1 (MQ=255)
                             gAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGCCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACtgtg                                                                                              >  1:49309/1‑109 (MQ=255)
                                aGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                   >  1:120451/1‑101 (MQ=255)
                                aGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                   <  2:120451/101‑1 (MQ=255)
                                  ccGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCActct                                                           <  1:343735/139‑1 (MQ=255)
                                             aatgaaGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTg                                                <  2:140676/139‑1 (MQ=255)
                                                      acgctgacgctgAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGa                                       <  1:63824/139‑1 (MQ=255)
                                                       cgctgacgctgaACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGaa                                      >  1:506194/1‑139 (MQ=255)
                                                                   aCGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATaa                          <  1:176824/139‑1 (MQ=255)
                                                                                  ccacGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTc           <  1:435573/139‑1 (MQ=255)
                                                                                    acGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTc                                                     <  1:123756/95‑1 (MQ=255)
                                                                                    acGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTc                                                     >  2:123756/1‑95 (MQ=255)
                                                                                     cGGATGTCATTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCAGCTGGAATATCCCCGATAACGCCACGGTGCAGTCggt        >  2:89895/1‑139 (MQ=255)
                                                                                             aTTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                   >  2:427507/1‑40 (MQ=255)
                                                                                             aTTGCTCAGCGCGGTACAGCCCCGAAGCTGACCGgcagca                                                                                                   <  1:427507/40‑1 (MQ=255)
                                                                                                    aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa  <  2:474231/130‑1 (MQ=255)
                                                                                                    aGCGCGGTACAGCCCCGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGa  >  1:474231/1‑130 (MQ=255)
                                                                                                                   |                                                                                                                  
CTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTACAGCCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGA  >  NC_000913/2073036‑2073265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A