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 |
|
A2 F999 I1 R1
|
226 |
132.7 |
9745491 |
85.7% |
8351885 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,957,092 |
+CC |
intergenic (+26/+58) |
ilvC → / ← ppiC |
ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,957,091 | 1 | . | C | 93.2%
| 141.4
/ 9.7
| 75 | intergenic (+25/+59) | ilvC/ppiC | ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C |
| Reads supporting (aligned to +/- strand): ref base . (4/1); new base C (30/39); total (35/40) |
| Fisher's exact test for biased strand distribution p-value = 1.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01 |
| * | NC_000913 | 3,957,091 | 2 | . | C | 93.3%
| 147.1
/ 9.7
| 75 | intergenic (+25/+59) | ilvC/ppiC | ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C |
| Reads supporting (aligned to +/- strand): ref base . (4/1); new base C (31/39); total (35/40) |
| Fisher's exact test for biased strand distribution p-value = 1.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
AAACTGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑CTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑GCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTG > NC_000913/3957016‑3957156
||
aaaCTGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑a > 1:1036642/1‑76 (MQ=255)
aaaCTGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑a > 2:1609463/1‑76 (MQ=255)
aCTGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑cc < 1:4011785/76‑2 (MQ=255)
cTGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑ccc < 2:1317807/76‑3 (MQ=255)
tGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑ccct < 2:1549275/76‑4 (MQ=255)
gcgcGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑Ccctc > 1:2368893/1‑76 (MQ=255)
cgcgGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑Ccctct < 2:1614209/76‑2 (MQ=255)
cgcgGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑Ccctct > 1:478764/1‑75 (MQ=255)
gcgGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑Ccctctc > 2:932293/1‑74 (MQ=255)
atatGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACag < 1:2119055/76‑1 (MQ=25)
atatGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACag < 1:4475856/76‑1 (MQ=25)
tatGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagg < 1:2122817/76‑1 (MQ=25)
atGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACaggg < 1:2214323/76‑1 (MQ=25)
tGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggc > 2:1830056/1‑75 (MQ=25)
gACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggag < 2:1416988/76‑1 (MQ=25)
aCAGATATGATACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCCCCCCG‑‑ACCCTCTCCCACagggaga < 2:3131647/76‑1 (MQ=21)
aCAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggaga > 2:4145504/1‑76 (MQ=21)
cAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggagag < 1:717806/76‑1 (MQ=21)
cAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggagag < 1:630200/76‑1 (MQ=21)
agagATGAAAGGTATTGCTGGTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggagagg < 2:932712/76‑1 (MQ=17)
aGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACagggagagg < 1:3440742/76‑1 (MQ=21)
atGAAACGTCTTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑AACCTCTCCCACAgggtgatggaga > 1:3199112/1‑76 (MQ=18)
atGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACA‑‑CTCTCCCACAgtgagagggaga > 1:3198734/1‑76 (MQ=21)
atGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAgggagagggaga > 1:3172230/1‑76 (MQ=18)
atGAAACGCATTGCTGTTGCGGGTTAGGTGCGCGCTGATGCCCTAACCCCG‑‑ACCCTCTCCCACAgagagagggaga > 1:4102153/1‑76 (MQ=17)
gAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGaaa < 2:3055993/76‑1 (MQ=18)
aaaCGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCCCCCCCCCCGGGCGAGGGAGaaaa > 2:691583/1‑76 (MQ=18)
aaaCGTATGGCTGGTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGaaaa < 2:122856/76‑1 (MQ=14)
aaCGTATTGCTGTTGCGCGTTAAGCGCGCGCTGATGCCCTCACCCCG‑‑ACCCCCTCCCACAGGCCGAGGCAGACAac > 2:468622/1‑76 (MQ=12)
aCGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAaca < 1:2103571/76‑1 (MQ=18)
cGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAacac > 2:2678528/1‑76 (MQ=18)
cGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAacac < 2:1188629/76‑1 (MQ=18)
tATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑c < 2:4735577/76‑1 (MQ=18)
aTTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑a < 1:1811970/76‑1 (MQ=18)
tGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑g > 1:4414096/1‑76 (MQ=18)
gCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑gg > 1:2133084/1‑75 (MQ=17)
gCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑gg < 2:2305205/76‑2 (MQ=17)
gCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑gg < 2:3756495/76‑2 (MQ=17)
cTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑ggc < 1:4433576/76‑3 (MQ=17)
tGTTGCGGGTTAAGGGCGCGCTGATGCCCTCACCCCG‑‑ACCCGCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑ggcc > 1:703250/1‑73 (MQ=17)
tGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtc > 2:1941298/1‑76 (MQ=14)
tGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtc < 2:2925065/76‑1 (MQ=14)
gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct > 1:955500/1‑76 (MQ=14)
gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct > 2:2722957/1‑76 (MQ=14)
gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct < 2:1612000/76‑1 (MQ=14)
gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct < 2:2368892/76‑1 (MQ=14)
cGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtctc < 1:2565759/76‑1 (MQ=14)
cGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtctc > 1:2074472/1‑76 (MQ=14)
gggTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTcc > 1:2235355/1‑76 (MQ=14)
gggTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTcc > 1:1461407/1‑76 (MQ=14)
gggTTAAGTGCGCGCTGATGACCTCACACCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTcc > 1:901981/1‑76 (MQ=14)
ggTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCt < 2:3257407/76‑1 (MQ=14)
ggTTAAGTGCGCGCTGATGCCCGCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGCACACACT‑C‑AAGGCCTTCTCCt < 2:703250/76‑1 (MQ=14)
tAAGTGCGCGCTGATGCCCTCTCCCCG‑‑ACCCTCTCCCACAGGTAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGga < 1:2589307/76‑1 (MQ=14)
aGTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACTCC‑AG‑GCCTTCTCCTGgaga > 1:3318988/1‑76 (MQ=14)
gTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGaa < 2:3931756/76‑1 (MQ=14)
gTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGaa < 2:426167/76‑1 (MQ=14)
gTGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGaa < 2:4635747/76‑1 (MQ=14)
tGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAg < 1:1973819/76‑1 (MQ=17)
tGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAg < 2:1289684/76‑1 (MQ=14)
tGCGCGCTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCCTCTCCTGGAGAAg > 2:990502/1‑76 (MQ=14)
ggcgcgcTGATGCCCTACCCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAg < 2:2198243/75‑1 (MQ=14)
cgcgcTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGCAGGc > 2:1746703/1‑76 (MQ=14)
gcgcTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑CAAA‑GCCTGCTCCTGGAGAAGGcc > 1:883833/1‑76 (MQ=17)
gcgcTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGcc > 2:1309370/1‑76 (MQ=17)
gcgcTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGcc > 1:3941187/1‑76 (MQ=17)
cgcTGATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCt > 1:1166489/1‑76 (MQ=17)
tcggATGCCCTGACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCtt < 1:700137/73‑1 (MQ=17)
gcTGATGCCCTCACCGCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCtt < 1:956227/76‑1 (MQ=17)
gATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCt < 1:4145504/76‑1 (MQ=18)
gATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCt < 2:832927/76‑1 (MQ=18)
gATGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCt > 1:1322609/1‑76 (MQ=18)
aTGCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTa < 2:2774749/76‑1 (MQ=18)
gCCCTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTAtt < 2:1682834/76‑1 (MQ=18)
ccTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAg > 1:3385060/1‑76 (MQ=21)
cTCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGt > 1:3049342/1‑76 (MQ=21)
tCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGtt > 2:4365379/1‑76 (MQ=21)
tCACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGtt > 1:1918893/1‑76 (MQ=21)
ccACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGtt < 2:684935/75‑1 (MQ=21)
cACCCCG‑‑ACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTg > 1:1400570/1‑76 (MQ=25)
||
AAACTGCGCGGCTATATGACAGATATGAAACGTATTGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCG‑‑A‑‑CTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑GCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTG > NC_000913/3957016‑3957156
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
