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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | . | 97.1%
| 135.8
/ ‑1.1
| 35 | coding (1253/2187 nt) | espL4 | type III secretion system effector EspL4 |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base . (11/23); total (12/23) |
| Fisher's exact test for biased strand distribution p-value = 3.43e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.16e-01 |
TACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTT > NZ_CP009273/4211078‑4211246
|
tACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAttttt > 1:1046214/1‑90 (MQ=255)
acaTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcg < 1:1445499/90‑3 (MQ=255)
acaTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcg < 2:722021/90‑3 (MQ=255)
aTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcgag < 1:934916/90‑5 (MQ=255)
aTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcgag > 2:195905/1‑86 (MQ=255)
tATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTaa < 1:1294825/90‑1 (MQ=255)
tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc < 2:865398/90‑1 (MQ=255)
cTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCt > 1:549017/1‑90 (MQ=255)
tACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCtt > 2:1216123/1‑90 (MQ=255)
tACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTc > 2:828936/1‑90 (MQ=255)
gATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑‑TTTTTTCGAGAGTAATCCTTCATATcc < 1:387816/90‑1 (MQ=255)
tCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGt > 2:108728/1‑90 (MQ=255)
cGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGtt > 2:1484146/1‑90 (MQ=255)
aaaaaTAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTg > 2:1302112/1‑90 (MQ=255)
ataatCCAGAAGAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACaa < 1:1356479/90‑1 (MQ=255)
ataatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACaa < 2:890052/90‑1 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg < 2:288370/90‑1 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg > 1:1341045/1‑90 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg < 2:868005/90‑1 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCAAGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg < 1:45906/90‑1 (MQ=255)
atCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGa > 2:215043/1‑90 (MQ=255)
atCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGa > 2:120098/1‑90 (MQ=255)
tCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGaa > 1:1161632/1‑90 (MQ=255)
gAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGa > 1:1321413/1‑90 (MQ=255)
aaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAt < 1:637077/90‑1 (MQ=255)
ccATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAg < 1:1454686/90‑1 (MQ=255)
tttttATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGtct < 2:1572825/90‑1 (MQ=255)
tttttATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGtct < 1:1506299/90‑1 (MQ=255)
ttATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCaa < 2:1341045/90‑1 (MQ=255)
tATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAAc < 1:448029/90‑1 (MQ=255)
tATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAAc < 2:486893/90‑1 (MQ=255)
ttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATc < 1:1458431/90‑1 (MQ=255)
tGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATcc < 2:618832/90‑1 (MQ=255)
ccTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGc < 1:622287/90‑1 (MQ=255)
tCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAt < 1:1302112/90‑1 (MQ=255)
ccAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAtt < 2:1345559/90‑1 (MQ=255)
ccAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAtt < 1:231698/90‑1 (MQ=255)
atatGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCAt < 2:767330/90‑1 (MQ=255)
tatGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATa < 2:1435944/90‑1 (MQ=255)
cATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAAttt > 2:95294/1‑90 (MQ=255)
|
TACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTT > NZ_CP009273/4211078‑4211246
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA > NZ_CP009273/4211082‑4211249
|
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCC < SRR3722078.1469058/100‑1 (MQ=60)
CATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCT > SRR3722078.555502/1‑100 (MQ=60)
ATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTT < SRR3722078.947854/100‑1 (MQ=60)
TATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATAT < SRR3722078.1315449/100‑1 (MQ=60)
GATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑‑TTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGAC < SRR3722078.392541/100‑1 (MQ=60)
CGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATG > SRR3722078.1362558/1‑100 (MQ=60)
CTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAA > SRR3722078.1179638/1‑100 (MQ=60)
AAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGA > SRR3722078.1342534/1‑100 (MQ=60)
ATAATCCAGAAGAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAA < SRR3722078.1378258/100‑1 (MQ=60)
AATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCAAGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTTAAAAT < SRR3722078.46449/100‑1 (MQ=60)
AACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACG < SRR3722078.644399/100‑1 (MQ=60)
CCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGAT < SRR3722078.1478407/100‑1 (MQ=60)
ATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTnnnnnnnnnnnnnnnnnnnn > SRR3722078.1107425/1‑80 (MQ=60)
TTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATC < SRR3722078.1530862/100‑1 (MQ=60)
gatgtgtataagagacagGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCC < SRR3722078.928558/82‑1 (MQ=60)
TATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCA < SRR3722078.453388/100‑1 (MQ=60)
TTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCA < SRR3722078.1482218/100‑1 (MQ=60)
CCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAA < SRR3722078.629452/100‑1 (MQ=60)
TCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATT < SRR3722078.1322877/100‑1 (MQ=60)
CCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTT < SRR3722078.234509/100‑1 (MQ=60)
GAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATctgtctcttatacacatctgacgctgccgacgatggcggtcgtgtagatctcggtggtcgcc > SRR3722078.195246/1‑38 (MQ=60)
GAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA > SRR3722078.619101/1‑100 (MQ=60)
|
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA > NZ_CP009273/4211082‑4211249
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
