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
A12 F52 I0 R1 83 172.7 3180974 97.2% 3091906 265.9

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_0009132,066,4650TC78.9% 14.5 / ‑3.6 17K286R (AAG→AGG) insH1IS5 transposase and trans‑activator
Reads supporting (aligned to +/- strand):  ref base T (1/3);  new base C (5/8);  total (6/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCTCCA‑CCTTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTG  >  NC_000913/2066374‑2066748
                                                                                            |                                                                                                                                                                                                                                                                                           
cGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACTAAGCCCAACGGCCGCATGATCATGCCAAATGGGTGCTCCA‑ACTAGGCCCGGATGCTGGCTTTCATCTTTTCATTGTTAATGGGCTTTCTGCTATTAGTTGGATCCTGTTTCGAGGTTCTTATCTTGCATGGGCGCTCGGCGATCACCCAGTGCAAACACACCTCGGACAGCTCCACGAGCTGCGGCGCCCCTGGGAGCCCGGCATCGGCTCAGaaaatatggtcccttccgttcgagata                                                                                        >  2:956761/1‑266 (MQ=2)
    tatttgtgaacGTTTGTAAGCAAGCCCTTGTAGCTGGCTTTCACGAATCCCAACGCGCTCTTGATGTTGAGACATGGGTGCTCCA‑CCTGGGCCCGGATGCTGGCTTTCATGTATTCGTTGGTGATGGCCGTTTTATTCTTGCGTGGATGCTGTTTCACGGTTCTTACCTTGCCGTGGCGCTCTGCGATCAGCCAGTCCACTTCCACCTCTGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTAc                                                                                    <  2:457361/279‑1 (MQ=11)
                                  tATCTGGCTTTCACGAAGCCTAACTGTCTCTTGATTATGCGAAAGGGGTGCTCCA‑CCTTGGCCCGGTTTCTGTCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTTGATGCTGTTTAAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCcg                                                      <  2:672555/289‑1 (MQ=255)
                                                              gCTTGTTGTTGCGAACTGGGTG‑TCCAGCCTTGGCCCTGGTGCTGGCTTGCATGTATTCGATGTTGATGGCCGTTTGATTCTGGCGTGGATGCTGTTTCAAGTTTCTTACGTTGCCCGGGCGCTCGGCGTTCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTCGCGCCGCTTGGTAGCCGGCATCGGCTGAGACAAATTTCTCCTCTCCATGGAGCAGATTACCCAGCTGATTGGGGTCATGCTCGTTGGCCGCGGTGGTGACGAGGCTGTGGGTCAGGcc                          <  2:1220792/289‑1 (MQ=11)
                                                                        gCGAAATGGGTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCa                >  1:1390514/1‑289 (MQ=14)
                                                                        gCGAAATGGGTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCAAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTTGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAACTTGCTCCTCTCCATGCACCAGATTACCCAACTGACTGAGGTCATGCTCGTTGGACGCGGGGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGc                 >  1:1510870/1‑288 (MQ=255)
                                                                          gAATTGGGTGCTCCA‑CCCGGGCCCGGGTGCTGTCTTGCATTTATTCGATGTTGTTGGCAGTTTTGTTCTTGCGTGTATGCTGTTTCAAGGTTCTCAGCGTGGCGGGCCGCTCGGCGATTGGCCAGTCCAAATCCACCTCCGCCAGCTCCTCGCGCTGTGGCGCCCCTTGTTAGCCGGCATCGGCTGAGACCAATTGCTCCTCTGCATGCAGCAGAGTACCCAGCTGATTTAGGTCATGCTCGTTTGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt               <  2:1468159/288‑1 (MQ=255)
                                                                          gAAATGGGTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATc              <  1:862522/289‑1 (MQ=14)
                                                                          gAAATGGGTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGATCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCAt               <  1:1423685/288‑1 (MQ=14)
                                                                             aTGGGTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGac           <  1:792999/289‑1 (MQ=14)
                                                                              tGGGTGCTCCA‑CCCTGGCCCGGTTGCTGTCTTGCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCCGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGaca          <  1:715266/289‑1 (MQ=9)
                                                                               gggTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGacac         <  1:593455/289‑1 (MQ=14)
                                                                               gggTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGacac         <  1:1291282/289‑1 (MQ=14)
                                                                                 gTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCa       >  1:1433872/1‑289 (MQ=14)
                                                                                 gTGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGAGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGGATCGCAACCa       >  1:1568707/1‑289 (MQ=9)
                                                                                  tGCTCCA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCCCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGGGGGTCCGGCCGATCTTGGCATCGaaccc        >  2:323856/1‑283 (MQ=9)
                                                                                      ccA‑CCCTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAAtgcg  <  1:1234286/289‑3 (MQ=14)
                                                                                            |                                                                                                                                                                                                                                                                                           
CGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGCTTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCTCCA‑CCTTGGCCCGGATGCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAAGGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTCCTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATGCAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTG  >  NC_000913/2066374‑2066748

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A