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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,584,697 |
T→C |
40.8% |
L860L (CTA→CTG) |
mdtF ← |
multidrug transporter, RpoS‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,584,697 | 0 | T | C | 40.8%
| 16.6
/ 32.8
| 49 | L860L (CTA→CTG) | mdtF | multidrug transporter, RpoS‑dependent |
| Reads supporting (aligned to +/- strand): ref base T (16/13); new base C (6/14); total (22/27) |
| Fisher's exact test for biased strand distribution p-value = 1.43e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.63e-01 |
GAAATCGCATACAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCTGCCATAAATTTCATG > minE/2584644‑2584763
|
gAAATCGCATACAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATg > 1:432159/1‑67 (MQ=255)
aaaTCGCATACAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGt > 1:1632075/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:1028250/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:260839/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:2528871/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:2833152/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:2083813/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:2961702/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:3312102/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:1585927/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:333627/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:1338621/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:1334671/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:3356509/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGcc > 1:349801/1‑69 (MQ=255)
cAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGc > 1:403602/1‑68 (MQ=255)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:3315649/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:3243130/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:3091190/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:2971150/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:3354596/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:290801/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:2820601/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:1036138/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:2769439/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:2735108/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:1037858/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:1083554/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:2279355/46‑1 (MQ=38)
gggAGCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTcc < 1:2343125/46‑1 (MQ=38)
gCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGt > 1:1975885/1‑69 (MQ=255)
gCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGt > 1:908254/1‑69 (MQ=255)
gCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGt > 1:1547217/1‑69 (MQ=255)
gCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGt > 1:1476672/1‑69 (MQ=255)
gCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGt > 1:1233600/1‑69 (MQ=255)
gCCTGGTTTGAGGATAACGCTTCCTGATACGACAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGt > 1:2775118/1‑69 (MQ=255)
ttGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGc < 1:2245450/67‑1 (MQ=255)
ttGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGc < 1:2949164/67‑1 (MQ=255)
ttGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGc < 1:1996187/67‑1 (MQ=255)
tGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGAc < 1:2885577/69‑1 (MQ=255)
tGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGAc < 1:1149449/69‑1 (MQ=255)
aaCGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:1061559/69‑1 (MQ=255)
aCGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:2743779/68‑1 (MQ=255)
aCGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:91989/68‑1 (MQ=255)
aCGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:989998/68‑1 (MQ=255)
aCGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:67913/68‑1 (MQ=255)
aCGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:1715027/68‑1 (MQ=255)
aCGCTTCCTGATACGATAGTCCGGGCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCt < 1:191224/68‑1 (MQ=255)
aTAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCTGCCATAAATTTCATg < 1:1930687/68‑1 (MQ=255)
|
GAAATCGCATACAGCGCAGGAGCCTGATTTGAGGATAACGCTTCCTGATACGATAGTCCGGTCCATGAGTAGCCGACGCCTGCCGGAAGTTTAGCGACCAGGTCTGCCATAAATTTCATG > minE/2584644‑2584763
|
| 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
