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
A13 F19 I0 R1 47 161.4 2832088 96.9% 2744293 271.8

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_0009132,066,4650TC87.6% 11.4 / ‑5.3 13K286R (AAG→AGG) insH1IS5 transposase and trans‑activator
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (3/8);  total (4/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
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.

CTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCT‑CCACCTTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGG  >  NC_000913/2066188‑2066749
                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                                                            
ctaggCTGACCCAGTTATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCACCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCTCACTGACGTATCATTTGGTCCCCCCGAAACTGGTTGGCCAGCTTAAATAACTTCGCCTGTTGGTTATCGTTTTTCAGCACCTTCGTTTTTCTGTCTTTCTCCAATCACAACATTCTTTTCATGAACCTAAATGGATGCT‑CGACCTTGGACCgttt                                                                                                                                                                                                                                                                                    >  2:1082462/4‑285 (MQ=11)
                                                                                                                                                                                                                              tctacgttgaaCGCAGCCTAACTGTCGCTTGATCATGCGAAATGGGTGCTCCCACCTT‑GCCTGGATTCTGGCTTTCATGGATTCGATGTTTACGGCCGTTTTGTTCTTGCTAGGATGCTGTTTCAGGTTTCTAACCTGCCCGGGGCGTGCGGCGTTCAGCCGGTCCACATCCACCTCGGCCAGCCCCTCACGCTGTGCCGCCCCTTGGTATCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATGACCCAGCTGATTGAGGTCATGCTCGTAGGCcgcg                                                     <  2:703980/279‑1 (MQ=1)
                                                                                                                                                                                                                                                           tgatgaTGCGAAATGGGTGCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGc                         >  1:680439/1‑288 (MQ=11)
                                                                                                                                                                                                                                                                agacGAAATGGGTTCG‑CCACCCTGGCCGGGATGCTTGCTTTCATGTAGTGGATGTGGCTGGCCTTTGTGTGCTTGCGTGGTTGATGTTTGAAGGTTCTTGCCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACTGCCACCTCGGCCAGCTCCTCGCGCTTTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTg                    <  2:890936/285‑1 (MQ=11)
                                                                                                                                                                                                                                                                    gAAATGGGTGCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt                <  1:1090865/288‑1 (MQ=14)
                                                                                                                                                                                                                                                                    gAAATGGGTGCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt                <  1:409002/288‑1 (MQ=14)
                                                                                                                                                                                                                                                                    gAAATGGGTGCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt                <  1:692629/288‑1 (MQ=14)
                                                                                                                                                                                                                                                                      aaTGGGTGCA‑CGCCCCTGGCCCGGTTGTTGGTTTTCATGTATTTGATGTTGATGGCCTTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTGGGCGATCAGCCATTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGa             <  2:431629/289‑1 (MQ=11)
                                                                                                                                                                                                                                                                       aTGGGTGCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGac            <  1:922783/289‑1 (MQ=14)
                                                                                                                                                                                                                                                                        tGGGTGCT‑CCACCCTGGCCCGGGTGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTGGGCATCGaca           <  1:393310/289‑1 (MQ=14)
                                                                                                                                                                                                                                                                            tGCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCGCGTTGGCCGCTGTGGTGACTAGGCTGTGGTTCAGGCCGCTCTTGGCCTCGACACCaa       >  2:401482/1‑289 (MQ=9)
                                                                                                                                                                                                                                                                             gCT‑CCACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCCTTTGGCATCGACCCCAAt      >  1:1221599/1‑289 (MQ=14)
                                                                                                                                                                                                                                                                                  cACCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTgg  <  2:722166/289‑1 (MQ=14)
                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                                                            
CTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTTGGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCT‑CCACCTTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGG  >  NC_000913/2066188‑2066749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A