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 F116 I0 R1
|
44 |
26.4 |
562224 |
96.5% |
542546 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,087,670 |
A→T |
79.2% |
L5I (TTA→ATA) |
USA300HOU_1021 ← |
hypothetical membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,087,670 | 0 | A | T | 79.2%
| 45.3
/ 8.4
| 24 | L5I (TTA→ATA) | USA300HOU_1021 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (2/3); new base T (12/7); total (14/10) |
| Fisher's exact test for biased strand distribution p-value = 6.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
AAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCAGGTT > CP000730/1087538‑1087805
|
aaaCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTg < 1:266790/141‑1 (MQ=255)
aaaCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTg > 2:118848/1‑141 (MQ=255)
aCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCCCACCATTGTAATCAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGAc > 1:263839/1‑141 (MQ=255)
aCCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACCCAATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGAc > 1:263863/1‑141 (MQ=255)
gTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACAtttt > 2:165969/1‑141 (MQ=255)
tGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATaaaaa > 2:118279/1‑141 (MQ=255)
aaGGCCTGTAGCTTGCACACCATTGTCAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATaaaaaaa < 1:169307/141‑1 (MQ=255)
cATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACAATCCATAGGaa > 2:178453/1‑141 (MQ=255)
aaacaaacCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTAt < 1:118848/141‑1 (MQ=255)
aacaaacCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATg < 1:118279/141‑1 (MQ=255)
ccaTAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACaa < 1:221653/141‑1 (MQ=255)
ccaTAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACaa > 2:169947/1‑141 (MQ=255)
tAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGCAATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCAATAGGAAAGTTATGCGTTCACAATATATATTAGTaaa > 2:12439/1‑141 (MQ=255)
cTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACa < 1:152873/141‑1 (MQ=255)
gAAGACTACTGAAATAATGACGGTTACTAGTATTTCAGATAGCTTCAAACCTTCTGACATTTCTACAGCCTCCTAATAAAAAAACGCACAACCTTCCATAGGAAAGTTATGCGTTCACAATATATATTAGtcacccatgcg < 2:2793/141‑11 (MQ=255)
aTACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACCTCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGATATGCGTTCACAATATATATTAGTAAAACATATGta > 2:218769/1‑141 (MQ=255)
aTACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCCCAAAATATATTAGTAAAACattagtt > 2:103769/1‑136 (MQ=255)
tACTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAg < 1:165969/141‑1 (MQ=255)
aCTAGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGt > 1:197414/1‑141 (MQ=255)
caGTATTTCAGATAGCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTc < 1:261812/140‑1 (MQ=255)
tttCAGATAGCTTTATACCTTTCGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCt < 1:85705/141‑1 (MQ=255)
gCTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCAGGt > 2:36165/1‑141 (MQ=255)
cTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATGGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCAGGtt > 1:233379/1‑141 (MQ=255)
cTTTATACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAAAATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGAGTAGGtt > 1:233350/1‑141 (MQ=255)
|
AAACCCCGTTTGTTAATTGTTCGAGGTGAAGGCCTGTAGCTTGCACACCATTGTAAACAAACCACCATAAATTGTAAATAACTGCGAATACTACTGAAATAAGTACGGTTACTAGTATTTCAGATAGCTTTAAACCTTTTGACATTTTTACATCCTCCTAATAAAAAAACGCACAACCATCCATAGGAAAGTTATGCGTTCACAATATATATTAGTAAAACATATGTATAGTAACACTTTCCTACGCTAGTTCAAGCTAGATCAGGTT > CP000730/1087538‑1087805
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
