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 |
2,819,095 |
T→C |
intergenic (‑160/‑96) |
mltB ← / → srlA |
lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,819,095 | 0 | T | C | 100.0%
| 125.2
/ NA
| 38 | intergenic (‑160/‑96) | mltB/srlA | lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/16); total (22/16) |
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAA > NZ_CP009273/2819012‑2819180
|
cTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCAtttt > 2:800396/1‑90 (MQ=255)
tGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTg > 2:120131/1‑90 (MQ=255)
gATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATc < 2:1542272/90‑1 (MQ=255)
gATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATc < 1:120131/90‑1 (MQ=255)
gATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATc < 2:352567/90‑1 (MQ=255)
aTACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCa > 2:959887/1‑90 (MQ=255)
aTACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCa < 2:108247/90‑1 (MQ=255)
cGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCaaaa > 1:717621/1‑90 (MQ=255)
gACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATa > 1:397500/1‑90 (MQ=255)
cTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAac < 2:995724/90‑1 (MQ=255)
ttACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAacac > 1:1151920/1‑90 (MQ=255)
ttACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAacac > 2:1111875/1‑90 (MQ=255)
tACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACt > 2:1015829/1‑90 (MQ=255)
actcaactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaaa < 1:1059240/90‑1 (MQ=255)
actcaactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTaaa > 2:1220455/1‑90 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt > 2:73342/1‑90 (MQ=255)
caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt > 1:1230785/1‑90 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc > 1:356725/1‑90 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc < 1:1409438/90‑1 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc > 2:1547620/1‑90 (MQ=255)
ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc < 2:1557036/90‑1 (MQ=255)
cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt > 2:111604/1‑90 (MQ=255)
cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt > 2:1465367/1‑90 (MQ=255)
cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt > 2:1550804/1‑90 (MQ=255)
cTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgattagat > 2:32955/1‑90 (MQ=255)
ttttATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGtt < 2:1213228/90‑1 (MQ=255)
aTTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCg > 1:874316/1‑90 (MQ=255)
aTTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCg > 2:655796/1‑90 (MQ=255)
aTTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCg > 1:1467831/1‑90 (MQ=255)
aaaCTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTg < 1:1133383/90‑1 (MQ=255)
aaaCTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTg < 1:37762/90‑1 (MQ=255)
aaaTTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATaaa < 2:1302507/90‑1 (MQ=255)
aaaTTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATaaa < 2:1195326/90‑1 (MQ=255)
aaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATaa < 2:26357/90‑1 (MQ=255)
aaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATaa < 1:1495810/90‑1 (MQ=255)
tATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTg > 2:365567/1‑90 (MQ=255)
aTCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGa < 1:534031/90‑1 (MQ=255)
tCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGaa > 1:943661/1‑90 (MQ=255)
|
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAA > NZ_CP009273/2819012‑2819180
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GAAGCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAAC > NZ_CP009273/2818999‑2819189
|
GAAGCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCAT < SRR3722078.1172682/100‑1 (MQ=60)
CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAA > SRR3722078.726484/1‑100 (MQ=60)
GCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATA > SRR3722078.402324/1‑100 (MQ=60)
GATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACAC > SRR3722078.1169700/1‑100 (MQ=60)
GATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACAC < SRR3722078.121536/100‑1 (MQ=60)
TTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCT > SRR3722078.1250184/1‑100 (MQ=60)
ACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATC < SRR3722078.1075167/100‑1 (MQ=60)
ACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATC > SRR3722078.361077/1‑100 (MQ=60)
TTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATT < SRR3722078.1432302/100‑1 (MQ=60)
CTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCG > SRR3722078.1491776/1‑100 (MQ=60)
CTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCG > SRR3722078.886045/1‑100 (MQ=60)
AAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAAC < SRR3722078.1150743/100‑1 (MQ=60)
AAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAAC < SRR3722078.38215/100‑1 (MQ=60)
AAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAA > SRR3722078.956827/1‑100 (MQ=60)
AATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGG < SRR3722078.1520189/100‑1 (MQ=60)
ATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGTTTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGA > SRR3722078.774811/1‑100 (MQ=60)
ATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGA > SRR3722078.506987/1‑100 (MQ=60)
ATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAAC < SRR3722078.540342/100‑1 (MQ=60)
|
GAAGCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAGGAGAGAAC > NZ_CP009273/2818999‑2819189
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
