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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | . | 97.3%
| 144.3
/ ‑1.4
| 37 | coding (1253/2187 nt) | espL4 | type III secretion system effector EspL4 |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base . (9/27); total (10/27) |
| Fisher's exact test for biased strand distribution p-value = 2.70e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.52e-01 |
TACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTAT > NZ_CP009273/4211078‑4211248
|
tACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAttttt > 1:407556/1‑90 (MQ=255)
acaTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcg < 1:691398/90‑3 (MQ=255)
ttATCCTTACGTGATATCAGTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTa < 2:384414/90‑1 (MQ=255)
tATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTaa < 1:817498/90‑1 (MQ=255)
tATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTaa < 2:501645/90‑1 (MQ=255)
aTCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAAt < 1:244524/90‑1 (MQ=255)
tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAGTATGCATGAGA‑TTTTTTTCGAGAGTAATc < 1:689151/90‑1 (MQ=255)
tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc < 2:166667/90‑1 (MQ=255)
tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc < 1:98688/90‑1 (MQ=255)
tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc < 1:525344/90‑1 (MQ=255)
cTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCt > 2:536703/1‑90 (MQ=255)
ttACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCtt > 2:144390/1‑90 (MQ=255)
tACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTc > 2:77431/1‑90 (MQ=255)
cGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCat < 1:374833/90‑1 (MQ=255)
tCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGt > 1:19446/1‑90 (MQ=255)
gCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGttt > 2:160087/1‑90 (MQ=255)
aaaaTAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGa < 1:429347/90‑1 (MQ=255)
ataatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACaa < 1:144390/90‑1 (MQ=255)
taatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAAt < 2:636561/90‑1 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg < 2:258412/90‑1 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg < 1:77431/90‑1 (MQ=255)
aatCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg < 2:657845/90‑1 (MQ=255)
atCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATg > 1:173395/1‑90 (MQ=255)
tCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGaa > 1:612582/1‑90 (MQ=255)
gAAAAACCATTTTTATCTTTTGCCTCCAGATTATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGa > 1:29315/1‑90 (MQ=255)
aaaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGaaaa < 1:370442/90‑1 (MQ=255)
aaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAt < 1:554682/90‑1 (MQ=255)
aaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAt < 2:258149/90‑1 (MQ=255)
aaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAt < 2:398846/90‑1 (MQ=255)
ttttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGata < 1:132868/90‑1 (MQ=255)
ttttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGata < 2:603218/90‑1 (MQ=255)
tCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCCCAACGATATCCGCAt < 2:831690/90‑1 (MQ=255)
aaTATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCa < 2:405635/90‑1 (MQ=255)
atatGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCAt < 2:647999/90‑1 (MQ=255)
tGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATa > 2:425368/1‑62 (MQ=255)
tGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATa < 1:425368/62‑1 (MQ=255)
tGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTtat < 2:642891/90‑1 (MQ=255)
tGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTtat > 2:472940/1‑90 (MQ=255)
tGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTtat < 1:71604/90‑1 (MQ=255)
|
TACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTAT > NZ_CP009273/4211078‑4211248
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC > NZ_CP009273/4211082‑4211263
|
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCC < SRR3722079.698669/100‑1 (MQ=60)
TATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATAT < SRR3722079.826257/100‑1 (MQ=60)
ATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATC < SRR3722079.246583/100‑1 (MQ=60)
TCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAGTATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCC < SRR3722079.696398/100‑1 (MQ=60)
TCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCC < SRR3722079.99468/100‑1 (MQ=60)
TCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCC < SRR3722079.530217/100‑1 (MQ=60)
TTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGT > SRR3722079.19582/1‑100 (MQ=60)
CGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTC < SRR3722079.377868/100‑1 (MQ=60)
GCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATG > SRR3722079.174903/1‑100 (MQ=60)
CTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAA > SRR3722079.618778/1‑100 (MQ=60)
AAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTG < SRR3722079.433063/100‑1 (MQ=60)
AAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGATTATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGA > SRR3722079.29531/1‑100 (MQ=60)
ATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAA < SRR3722079.145630/100‑1 (MQ=60)
AATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAT < SRR3722079.78064/100‑1 (MQ=60)
AAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAAC < SRR3722079.373413/100‑1 (MQ=60)
AACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACG < SRR3722079.560022/100‑1 (MQ=60)
gatgtgtataagagacagCTCCAGAATATGTATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGA < SRR3722079.429040/82‑1 (MQ=60)
TTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTAC < SRR3722079.133976/100‑1 (MQ=60)
GAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA > SRR3722079.61128/1‑100 (MQ=60)
GAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA > SRR3722079.336460/1‑100 (MQ=60)
GAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATA > SRR3722079.770533/1‑100 (MQ=60)
TGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATAT < SRR3722079.72202/100‑1 (MQ=60)
TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC < SRR3722079.114361/100‑1 (MQ=60)
TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC < SRR3722079.277434/100‑1 (MQ=60)
|
ACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTATAGCCAAATATAAACC > NZ_CP009273/4211082‑4211263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
