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 |
1,782,276 |
T→G |
V192G (GTG→GGG) |
ppsR → |
posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,782,276 | 0 | T | G | 97.4%
| 119.9
/ ‑4.0
| 38 | V192G (GTG→GGG) | ppsR | posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (24/13); total (25/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
CCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGG > NZ_CP009273/1782193‑1782359
|
ccccACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAACCTACCCCTTCATTGCCGACGATATGGATAATCTGGGGCTAcc > 1:1524264/1‑90 (MQ=255)
ccaccaGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCcg > 2:1217061/1‑90 (MQ=255)
ccaGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGt < 2:720515/90‑1 (MQ=255)
gTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGc > 1:261223/1‑90 (MQ=255)
tGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCa > 2:1241380/1‑90 (MQ=255)
tCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAAcc < 2:361059/90‑1 (MQ=255)
tGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGc > 1:287433/1‑90 (MQ=255)
ggCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCt > 1:682289/1‑90 (MQ=255)
ggCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCt > 1:461250/1‑90 (MQ=255)
ggCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCt > 1:1428561/1‑90 (MQ=255)
gCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCtt < 1:499089/90‑1 (MQ=255)
gCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCtt < 1:1473539/90‑1 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTc > 1:543086/1‑78 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTc < 2:543086/78‑1 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAg > 2:34565/1‑90 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAg > 1:1205832/1‑90 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAg > 1:791918/1‑90 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAg > 1:774325/1‑90 (MQ=255)
gCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCa < 1:1047746/90‑1 (MQ=255)
tttGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATaaa < 1:320624/90‑1 (MQ=255)
tttGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATaaa < 1:72092/90‑1 (MQ=255)
cgcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGc > 2:310376/1‑90 (MQ=255)
cgcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTAcc > 1:129296/1‑53 (MQ=255)
cgcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTAcc < 2:129296/53‑1 (MQ=255)
cgcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGc > 1:947709/1‑90 (MQ=255)
gcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGcc < 2:626966/90‑1 (MQ=255)
aCTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCg < 1:1241380/90‑1 (MQ=255)
ccTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCgg > 2:233084/1‑90 (MQ=255)
ttATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTc < 1:1412479/44‑1 (MQ=255)
ttATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTc > 2:1412479/1‑44 (MQ=255)
ttATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAAc > 1:1173180/1‑90 (MQ=255)
cgacgaTATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTggc > 1:824624/1‑90 (MQ=255)
cgacgaTATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTggc > 1:1125720/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 1:295833/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 2:58448/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg < 1:1217061/90‑1 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 1:103661/1‑90 (MQ=255)
aTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAgg > 1:39107/1‑90 (MQ=255)
|
CCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGG > NZ_CP009273/1782193‑1782359
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
CGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAAC > NZ_CP009273/1782179‑1782373
|
CGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGC < SRR3722078.58569/100‑1 (MQ=60)
CGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGC < SRR3722078.520578/100‑1 (MQ=60)
GTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAACCTACCCCTTCATTGCCGACGATATGGATAATCTGGGGCTACC > SRR3722078.1549109/1‑100 (MQ=60)
TGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCC < SRR3722078.249427/100‑1 (MQ=60)
ACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGC > SRR3722078.264410/1‑100 (MQ=60)
AGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGC > SRR3722078.290940/1‑100 (MQ=60)
GTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCT > SRR3722078.466757/1‑100 (MQ=60)
GTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCT > SRR3722078.1451790/1‑100 (MQ=60)
GTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCT > SRR3722078.690245/1‑100 (MQ=60)
ccatcgtcggcagcgtcagatgtgtataagagacagAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTC < SRR3722078.1435408/64‑1 (MQ=60)
GTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCct > SRR3722078.549504/1‑98 (MQ=60)
GTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAG > SRR3722078.1224761/1‑100 (MQ=60)
GTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAG > SRR3722078.784338/1‑100 (MQ=60)
GTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAG > SRR3722078.802292/1‑100 (MQ=60)
GCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAAT < SRR3722078.1497580/100‑1 (MQ=60)
GCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAAT < SRR3722078.504996/100‑1 (MQ=60)
GCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTC < SRR3722078.1063431/100‑1 (MQ=60)
GTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCctgtctcttatacacatctgacgctgc > SRR3722078.130787/1‑73 (MQ=60)
GTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGC > SRR3722078.960983/1‑100 (MQ=60)
TTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCC < SRR3722078.324548/100‑1 (MQ=60)
TTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCC < SRR3722078.72948/100‑1 (MQ=60)
AACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAAC > SRR3722078.1191448/1‑100 (MQ=60)
ACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACG < SRR3722078.1260990/100‑1 (MQ=60)
CCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGC > SRR3722078.1142936/1‑100 (MQ=60)
CCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGC > SRR3722078.835550/1‑100 (MQ=60)
CGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > SRR3722078.299442/1‑100 (MQ=60)
CGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > SRR3722078.104892/1‑100 (MQ=60)
GATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGG > SRR3722078.39576/1‑100 (MQ=60)
GGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGT > SRR3722078.1358446/1‑100 (MQ=60)
GGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGT > SRR3722078.1296245/1‑100 (MQ=60)
AATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGG < SRR3722078.1236196/100‑1 (MQ=60)
ATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGA > SRR3722078.75847/1‑100 (MQ=60)
GGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAAC < SRR3722078.409905/100‑1 (MQ=60)
GGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAAC < SRR3722078.657331/100‑1 (MQ=60)
GGGGCTAACCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGGCGGGAGGAC > SRR3722078.651771/1‑100 (MQ=60)
|
CGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAAC > NZ_CP009273/1782179‑1782373
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
