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
A15 F3 I0 R1 49 96.5 1638068 98.5% 1613496 272.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,066,465 T→C 100% K286R (AAG→AGG)  insH1 ← IS5 transposase and trans‑activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,066,4650TC87.8% 12.6 / ‑5.4 13K286R (AAG→AGG) insH1IS5 transposase and trans‑activator
Reads supporting (aligned to +/- strand):  ref base T (2/0);  new base C (2/9);  total (4/9)
Fisher's exact test for biased strand distribution p-value = 7.69e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCTCCACCTTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGG  >  NC_000913/2066202‑2066749
                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                                                              
tcatttcattTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTTAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCTCACCCTTGGCCCGGACGCTGGCCTTCCTGTa                                                                                                                                                                                                                                                                       >  1:723052/1‑289 (MQ=9)
                                                        gCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGGCGTCAACCTTGGCCGGGATGCTGACTTTCAGTTCTTCG‑TGTGTGA‑GGCCGTTTTTGTTTTTGGGTGGTTCTTGTTCCACGTTTCTTACCt                                                                                                                                                                                                             >  2:387079/1‑289 (MQ=11)
                                                                                                                                                                                                                                                      taaaTGGGTGCTCCACCCTGTCCCTGAGGCTGGCTTTAATGTATTCGAGGT‑TGCTGTCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt                <  1:385909/287‑1 (MQ=9)
                                                                                                                                                                                                                                                      gAAATGGGTGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt                <  2:555992/288‑1 (MQ=14)
                                                                                                                                                                                                                                                      gAAATGGGTGCCCCACCCTGGCCCGGATGCTGGCTTTCATTTATTCGTTGT‑TGATGGCCG‑TTTTGTTCTTGCTTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATc               <  1:398451/289‑1 (MQ=9)
                                                                                                                                                                                                                                                        aaTGGGTGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCg              >  2:51065/1‑288 (MQ=14)
                                                                                                                                                                                                                                                        aaTGGGTGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGa             <  2:132694/289‑1 (MQ=14)
                                                                                                                                                                                                                                                           gggTGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGacac          <  2:635748/289‑1 (MQ=14)
                                                                                                                                                                                                                                                            ggTGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGacac          <  1:325865/288‑1 (MQ=14)
                                                                                                                                                                                                                                                            ggTGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGacac          <  2:81257/288‑1 (MQ=14)
                                                                                                                                                                                                                                                              tGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCa        <  2:647717/288‑1 (MQ=14)
                                                                                                                                                                                                                                                              tGCTCCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCCGTGGGTCAGGCCGCTCTTGGCATCGACACCaa       >  1:753300/1‑289 (MQ=14)
                                                                                                                                                                                                                                                                   cACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTgg  <  2:536137/289‑1 (MQ=14)
                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                                                              
TCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCTCCACCTTGGCCCGGATGCTGGCTTTCATGTATTCGATGT‑TGATGGCCG‑TTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGG  >  NC_000913/2066202‑2066749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A