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 |
2,003,480 |
T→C |
F60S (TTC→TCC) |
yedK → |
SOS response‑associated peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,003,480 | 0 | T | C | 93.5%
| 124.5
/ ‑0.5
| 46 | F60S (TTC→TCC) | yedK | SOS response‑associated peptidase |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (24/19); total (25/21) |
| Fisher's exact test for biased strand distribution p-value = 5.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.62e-01 |
CCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTT‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003395‑2003566
|
cccATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTgg < 2:916731/90‑1 (MQ=255)
aTTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGa > 2:311500/1‑90 (MQ=255)
aTTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGa > 2:1009220/1‑90 (MQ=255)
cAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGc < 2:1407156/90‑1 (MQ=255)
gATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTc > 2:548618/1‑90 (MQ=255)
cAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCgg < 2:989618/90‑1 (MQ=255)
gTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGAtgg < 2:1255011/90‑1 (MQ=255)
gTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGAtgg < 1:1557731/90‑1 (MQ=255)
tCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGAtggt < 1:480790/90‑1 (MQ=255)
gcgtCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGAtggtgg > 1:1211111/1‑90 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGatat > 2:1104705/1‑75 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGatat < 1:1104705/75‑1 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGAtggtgg > 2:1191523/1‑90 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGAtggtgg > 1:1185149/1‑90 (MQ=255)
gAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAAc > 2:1535859/1‑90 (MQ=255)
aaGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACcgccgc < 2:1211111/90‑1 (MQ=255)
gCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGc > 2:305899/1‑90 (MQ=255)
gCTCAGTGAACGTGATGAACACCTTCATATGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGc > 1:191453/1‑90 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:305899/90‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 1:815112/1‑90 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGATGGGATAAACCGCCGCTGATTAACGccc < 1:311500/90‑1 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTT‑CTGGGGATATGCTCCCGGAtgg < 2:1129650/59‑1 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTT‑CTGGGGATATGCTCCCGGAtgg > 1:1129650/1‑59 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgcg > 2:1055500/1‑90 (MQ=255)
aaCGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAg > 2:1217078/1‑90 (MQ=255)
cGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:1164993/82‑1 (MQ=255)
cGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 2:1164993/1‑82 (MQ=255)
cGTGATGAACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGaa > 1:570398/1‑90 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGc > 2:661067/1‑90 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGc > 2:73443/1‑90 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGc > 1:269548/1‑90 (MQ=255)
ccTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATaa < 2:653020/51‑1 (MQ=255)
ccTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATaa > 1:653020/1‑51 (MQ=255)
ccTTCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAc > 1:1032259/1‑90 (MQ=255)
cTTCATCTGGATCCGTTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAcc < 1:23311/90‑1 (MQ=255)
cTTCATCTGGATCCGGTTTC‑CTGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAcc < 2:1165523/90‑1 (MQ=255)
tCATCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAg < 1:890816/90‑1 (MQ=255)
aTCTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTc > 2:462394/1‑90 (MQ=255)
cTGGATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGt < 1:311442/90‑1 (MQ=255)
cTGGATCCGGTTTC‑CTGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGt < 1:1196727/90‑1 (MQ=255)
gATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 2:1528723/61‑1 (MQ=255)
gATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 1:1528723/1‑61 (MQ=255)
gATCCGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATg > 2:719202/1‑90 (MQ=255)
gaccGGTTTTCCGGGGGATATCCCCCGGGATGGTGGGAAAACCCGCCGCTGATTAACCCCCGCGTAGAAACTGCGGCAACCAGTCGTATg < 1:830401/88‑1 (MQ=255)
ccGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 2:1103370/1‑58 (MQ=255)
ccGGTTTC‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:1103370/58‑1 (MQ=255)
tttc‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAc < 1:1535859/90‑1 (MQ=255)
|
CCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTT‑CTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003395‑2003566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ 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
CTATGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAACA > NZ_CP009273/2003382‑2003579
|
CTATGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCC > SRR3722078.6888/1‑100 (MQ=60)
CTATGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCC > SRR3722078.1101207/1‑100 (MQ=60)
CTATGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCC > SRR3722078.841771/1‑100 (MQ=60)
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGG < SRR3722078.1007038/100‑1 (MQ=60)
CCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGAT < SRR3722078.1231855/100‑1 (MQ=60)
CCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGAT < SRR3722078.1193192/100‑1 (MQ=60)
GACAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT < SRR3722078.1121547/100‑1 (MQ=60)
ATACAACGTCGCGTCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGG > SRR3722078.1230148/1‑100 (MQ=60)
ATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGG > SRR3722078.1203681/1‑100 (MQ=60)
GTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAAC < SRR3722078.1583087/100‑1 (MQ=60)
TCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACC < SRR3722078.486487/100‑1 (MQ=60)
AAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATATGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGC > SRR3722078.193728/1‑100 (MQ=60)
GTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATctgtctcttatacacatctgacgctgccgacgatggcggtcg > SRR3722078.1333149/1‑58 (MQ=60)
GTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCC > SRR3722078.825901/1‑100 (MQ=60)
CTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCtgtctcttatacacatctga > SRR3722078.1146942/1‑80 (MQ=60)
GCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGctgtctcttatacacatctgacgctgccgacgatggcggtcgggtagatctc > SRR3722078.180280/1‑48 (MQ=60)
GCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAA > SRR3722078.577078/1‑100 (MQ=60)
gtcagatgtgtataagagacagTCATCTGGATCCGGTTTCCGGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722078.1120182/78‑1 (MQ=60)
TCAGTGAACGTGATGAACCCCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722078.1183080/100‑1 (MQ=60)
TCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722078.309635/100‑1 (MQ=60)
TCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGATGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722078.315317/100‑1 (MQ=60)
GTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGC > SRR3722078.272842/1‑100 (MQ=60)
GTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGctgtctcttatacacatctgacgctgccg > SRR3722078.660501/1‑71 (MQ=60)
GTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAC > SRR3722078.1047593/1‑100 (MQ=60)
CCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACctgtctcttatacacatct > SRR3722078.1553629/1‑81 (MQ=60)
CTTCATCTGGATCCGTTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGT < SRR3722078.23605/100‑1 (MQ=60)
TCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTT < SRR3722078.902796/100‑1 (MQ=60)
CTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC < SRR3722078.315259/100‑1 (MQ=60)
CTGGATCCGGTTTCCTGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC < SRR3722078.1215496/100‑1 (MQ=60)
TTTCCTGGGGATATGCTCCCGGATGGGGGGAAAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCA < SRR3722078.1560893/100‑1 (MQ=60)
TTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAA > SRR3722078.148045/1‑100 (MQ=60)
TCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAAC > SRR3722078.553605/1‑100 (MQ=60)
CCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAACA > SRR3722078.1329386/1‑100 (MQ=60)
|
CTATGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAACA > NZ_CP009273/2003382‑2003579
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
