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 |
|
A19 F106 I0 R1
|
88 |
30.3 |
670850 |
93.2% |
625232 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
2,455,692 |
Δ1 bp |
100% |
coding (1210/1260 nt) |
USA300HOU_2315 → |
hypothetical membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,455,692 | 0 | G | . | 83.8%
| 114.7
/ 17.6
| 37 | coding (1210/1260 nt) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (1/0); major base . (20/11); minor base A (1/4); total (22/15) |
| Fisher's exact test for biased strand distribution p-value = 1.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
AGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAAC > CP000730/2455562‑2455828
|
agAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaattatc > 1:306352/1‑136 (MQ=255)
agAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaattata > 1:306294/1‑136 (MQ=255)
aaTCAGTTAAACAAGCGCGACAAAGTGGCGGTTTCCCAAAGGATTCAGAGGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATCAAGAAGACCGGCGTTCATCAGCTGTAGTGGATGGAGGATAAC‑TATCGa > 2:215140/1‑141 (MQ=255)
aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGaaaaa > 1:262910/1‑141 (MQ=255)
ttAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAAc > 1:209105/1‑141 (MQ=255)
aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGACCAATCtta > 1:139875/1‑140 (MQ=255)
aaGTGAAGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa < 1:71634/141‑1 (MQ=255)
aaGAGACGATTTAACAAAGGATTCCAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGGTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa < 2:130722/141‑1 (MQ=255)
gACGAGTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATa < 2:142485/141‑1 (MQ=255)
gATTTACCAAACGATTCAAACGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa < 1:189447/141‑1 (MQ=255)
cAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGCCCTATAAACAACAGTTACGTTCCACGCAGGTGATTGATGCA‑AAAAAAGTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg > 1:159648/1‑141 (MQ=255)
cAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg > 1:103083/1‑141 (MQ=255)
aGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc < 1:272661/141‑1 (MQ=255)
tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc < 1:118470/138‑1 (MQ=255)
tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAg > 1:89568/1‑141 (MQ=255)
tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAAAAATAATAACAAAGCGCTTGc > 2:118470/1‑138 (MQ=255)
gAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt < 2:7763/141‑1 (MQ=255)
agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAAACAAGCGCTACCTGGTAccacat > 2:282880/1‑137 (MQ=255)
tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa > 1:311178/1‑141 (MQ=255)
aTTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAga > 1:133896/1‑141 (MQ=255)
aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCACTTGATAGTACCTCTTAAAAAGATGATGCTAg > 1:274571/1‑141 (MQ=255)
aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCACTGGCGAGTACCTCTTAAAAAGATGATGCTAg > 1:274554/1‑141 (MQ=255)
ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc > 2:333057/1‑141 (MQ=255)
ctcGACTTAAAAAGACGACCGACGTTCATCAGTTGTAATCGATGCA‑AAAAAATTATCGAACACACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTTAAAAGATGATGCTAGCaa < 2:58315/139‑1 (MQ=255)
gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg < 1:107178/141‑1 (MQ=255)
gACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg < 2:311178/141‑1 (MQ=255)
aactcagaaaGAAGACATACGTTCATCAGTAGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAACATTCAGCTAAAAACAAATAATAACAAACCGCTTGCTAGTACCTCTTAAGAAGATTATGCTAGCAAgcg < 2:112524/134‑1 (MQ=255)
tgttaAAGAAGCCAGACGGTAAGCAGTTGTAATAGATGCAAAAAAAC‑TATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATATTAACGAAGCGTTTGTGAAAATCTCTAAAAAAGATGATGCTAGCAAGCGCtt < 2:2698/138‑1 (MQ=255)
ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACATCTTAAAAAGATGATACTAGCAGGCGCtttt > 1:106245/1‑141 (MQ=255)
aagaagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATCCTAACGAAGCGCGGGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta > 1:63012/1‑141 (MQ=255)
aagaagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta > 2:276461/1‑141 (MQ=255)
agacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGGGCTTTTctatact > 1:276604/1‑141 (MQ=255)
agacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACGGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact > 1:260426/1‑141 (MQ=255)
acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat > 1:270238/1‑141 (MQ=255)
agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat > 2:116678/1‑141 (MQ=255)
cGTTCATCAGATGTAATTAATGCA‑AAAAAATTATCGAAAAAACTGGAGTACAATGTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCCCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTACCCTAAAtatt > 2:331166/1‑141 (MQ=255)
gTTGATCGGGTGTAAGTGATGGAAAAAAAC‑GAGCGAGAAAACGGAGGAAAAATGTTCAAGTTAAAACAAATAAGAACAAAGCGCGTGCTAGTACCTCTTAAAAAGAAGATGCTAGCAAGCGCTTTTCTATACTATAtatta < 2:175745/141‑1 (MQ=255)
ataGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt < 2:81431/139‑1 (MQ=255)
aTGCAAAAAAA‑TTAGCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAac < 2:98076/141‑1 (MQ=255)
|
AGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAAC > CP000730/2455562‑2455828
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
