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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,572,896 |
C→T |
33.3% |
R171* (CGA→TGA) |
ompL → |
predicted outer membrane porin L |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,572,896 | 0 | C | T | 33.3%
| 85.7
/ 63.3
| 69 | R171* (CGA→TGA) | ompL | predicted outer membrane porin L |
| Reads supporting (aligned to +/- strand): ref base C (25/21); new base T (12/11); total (37/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01 |
GGCACCTACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAACACCTTCCGT > W3110S.gb/3572830‑3572961
|
ggCACCTACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGt > 1:2198078/1‑71 (MQ=255)
ggCACCTACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGt > 1:2276837/1‑71 (MQ=255)
ggCACCTACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGt > 1:424244/1‑71 (MQ=255)
ccTACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAAt < 1:1710613/71‑1 (MQ=255)
tACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGa > 1:1432658/1‑71 (MQ=255)
aCTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGAc > 1:244589/1‑71 (MQ=255)
ggAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACtt > 1:2266744/1‑70 (MQ=255)
ggAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACtt > 1:2069598/1‑70 (MQ=255)
aaTTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTaa < 1:8086/71‑1 (MQ=255)
aaTTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTaa < 1:2333214/71‑1 (MQ=255)
aaTTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTaa < 1:2727525/71‑1 (MQ=255)
aTTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTaa < 1:165647/70‑1 (MQ=255)
aTTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTaa < 1:2294403/70‑1 (MQ=255)
ttttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTg < 1:2636423/58‑1 (MQ=255)
ttttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTg < 1:1759957/58‑1 (MQ=255)
ttttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTaa > 1:2790972/1‑69 (MQ=255)
ttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTTAGTGAATGACTTTAAtag > 1:2769465/1‑70 (MQ=255)
ttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAAtag > 1:2222643/1‑70 (MQ=255)
ttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAAtag > 1:1232445/1‑70 (MQ=255)
ttAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAAtag > 1:1220104/1‑70 (MQ=255)
aTCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAAt < 1:1650878/63‑1 (MQ=255)
aTCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAAt < 1:2660571/63‑1 (MQ=255)
aCCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACgg > 1:1837621/1‑71 (MQ=255)
gATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTAAta > 1:308363/1‑58 (MQ=255)
gATAAATTTTCCTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTAAta > 1:315322/1‑58 (MQ=255)
aTAAATTTTCCTATACATTTGAGCCACATTACTTCATGc < 1:1451028/39‑1 (MQ=255)
tAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAg < 1:2329422/71‑1 (MQ=255)
aaaTTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGa > 1:346939/1‑67 (MQ=255)
ttCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGatcat < 1:1486140/70‑1 (MQ=255)
tCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGatcatc < 1:122253/70‑1 (MQ=255)
cTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTAAt < 1:1834313/46‑1 (MQ=255)
cTATACATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTAAt < 1:651176/46‑1 (MQ=255)
ataCATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTaa < 1:2158767/43‑1 (MQ=255)
taCATTTGAGCCACATTACTTCATGCGAGTGAATg > 1:969644/1‑35 (MQ=255)
taCATTTGAGCCACATTACTTCATGCGAGTGAATGACttt < 1:2537630/40‑1 (MQ=255)
taCATTTGAGCCACATTACTTCATGCGAGTGAATGACttt < 1:1766776/40‑1 (MQ=255)
cATTTGAGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGa > 1:2508939/1‑70 (MQ=255)
cATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGaa > 1:2512506/1‑55 (MQ=255)
cATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGaa > 1:647663/1‑55 (MQ=255)
cATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGaa > 1:1068097/1‑55 (MQ=255)
cATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTggg > 1:662736/1‑69 (MQ=255)
tttGAGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAAt < 1:915019/71‑1 (MQ=255)
tttGAGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAAt < 1:2156227/71‑1 (MQ=255)
tttGAGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAAt < 1:2622781/71‑1 (MQ=255)
tttGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAAt < 1:2452448/71‑1 (MQ=255)
tGAGCCACATTACTTCATGCGAGTGAATGACTTTAAtag > 1:2163592/1‑39 (MQ=255)
tGAGCCACATTACTTCATGCGAGTGAATGACTTTAAtag > 1:2541594/1‑39 (MQ=255)
tGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCa > 1:2106303/1‑71 (MQ=255)
aGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACt < 1:2282177/71‑1 (MQ=255)
aGCCACATTACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACt < 1:2758371/71‑1 (MQ=255)
aGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACt < 1:409342/71‑1 (MQ=255)
acaTTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGa < 1:1671361/44‑1 (MQ=255)
acaTTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAaca > 1:1995811/1‑71 (MQ=255)
caTTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGa < 1:739875/43‑1 (MQ=255)
caTTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGa < 1:2492159/59‑1 (MQ=255)
caTTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGa < 1:254534/59‑1 (MQ=255)
aTTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGatcatc < 1:2763640/51‑1 (MQ=255)
ttACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGatcatc < 1:1037074/50‑1 (MQ=255)
ttACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCa > 1:1500343/1‑62 (MQ=255)
ttACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAaca > 1:2019063/1‑68 (MQ=255)
ttACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGaa > 1:1857767/1‑58 (MQ=255)
ttACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAACACCt > 1:881149/1‑71 (MQ=255)
tACTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGat > 1:1082833/1‑45 (MQ=255)
aCTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTa > 1:1551566/1‑63 (MQ=255)
aCTTCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAACACCTTc > 1:1478578/1‑71 (MQ=255)
aCTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGAtcatca > 1:92698/1‑49 (MQ=255)
aCTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAACACCTTc > 1:936149/1‑71 (MQ=255)
ttCATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACt < 1:1177189/60‑1 (MQ=255)
cATGTGAGTGAATGACTTTAATAGTAGCAACGGGAAAGat > 1:1801337/1‑40 (MQ=255)
cATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAACACCTTCCGt > 1:1257475/1‑70 (MQ=255)
cGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGaaa > 1:1662836/1‑49 (MQ=255)
cGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGaaa > 1:2320102/1‑49 (MQ=255)
cGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTaa > 1:960754/1‑56 (MQ=255)
|
GGCACCTACTGGAATTTTAAAATCACCGATAAATTTTCCTATACATTTGAGCCACATTACTTCATGCGAGTGAATGACTTTAATAGTAGCAACGGGAAAGATCATCATTGGGAAATCACTAACACCTTCCGT > W3110S.gb/3572830‑3572961
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
