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 |
|
A1 F2 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,211,170 |
(T)8→7 |
coding (1246/2187 nt) |
espL4 ← |
type III secretion system effector EspL4 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,211,163 | 0 | T | . | 81.8%
| 19.7
/ 5.2
| 11 | coding (1253/2187 nt) | espL4 | type III secretion system effector EspL4 |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base . (3/6); total (4/7) |
| 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 |
TACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTAT > NZ_CP009273/4211078‑4211248
|
tACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAttttt > 1:206257/1‑90 (MQ=255)
aTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcgag < 1:378475/90‑5 (MQ=255)
tttATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGt < 2:568343/90‑1 (MQ=255)
tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc < 2:141538/90‑1 (MQ=255)
ataatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACaa < 1:538929/90‑1 (MQ=255)
aaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAt < 2:233025/90‑1 (MQ=255)
cTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTaa < 1:399552/42‑1 (MQ=255)
cTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTaa > 2:399552/1‑42 (MQ=255)
ccAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAt < 1:306772/90‑1 (MQ=255)
ccAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAtt > 1:369460/1‑90 (MQ=255)
ccAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAtt < 2:121018/90‑1 (MQ=255)
atGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCGTATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATaa > 2:237753/1‑90 (MQ=255)
gagaTTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTtat > 1:511825/1‑90 (MQ=255)
|
TACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTAT > NZ_CP009273/4211078‑4211248
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC > NZ_CP009273/4211084‑4211263
|
ATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTT < SRR3722111.383894/100‑1 (MQ=60)
gacattcgtcggcagcgtcagatgtgtataagagacagCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATAT < SRR3722111.405371/62‑1 (MQ=60)
ATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAA < SRR3722111.547397/100‑1 (MQ=60)
TCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATT > SRR3722111.374684/1‑100 (MQ=60)
CCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATT < SRR3722111.310764/100‑1 (MQ=60)
GAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTAT > SRR3722111.519769/1‑100 (MQ=60)
ATTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAAC < SRR3722111.64695/100‑1 (MQ=60)
TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC < SRR3722111.324985/100‑1 (MQ=60)
|
ATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC > NZ_CP009273/4211084‑4211263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
