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 |
2,089,147 |
A→G |
47.8% |
A90A (GCT→GCC) |
yhaJ ← |
predicted DNA‑binding transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,089,147 | 0 | A | G | 47.8%
| ‑3.5
/ 38.8
| 46 | A90A (GCT→GCC) | yhaJ | predicted DNA‑binding transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base A (14/10); new base G (9/13); total (23/23) |
| Fisher's exact test for biased strand distribution p-value = 3.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.83e-01 |
AAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCCAACA > minE/2089079‑2089208
|
aaaaaGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCgaga > 1:856301/1‑69 (MQ=255)
aaaaaGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCgaga > 1:2615469/1‑69 (MQ=255)
aaaaaGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCgaga > 1:1810129/1‑69 (MQ=255)
aaaaaGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCgaga > 1:1806071/1‑69 (MQ=255)
gtCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATc > 1:3055676/1‑68 (MQ=255)
gtCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATc > 1:214884/1‑68 (MQ=255)
aCCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTc > 1:1174354/1‑69 (MQ=255)
aCCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTc > 1:1244449/1‑69 (MQ=255)
aCCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTc > 1:2782391/1‑69 (MQ=255)
aCCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTc > 1:1474481/1‑69 (MQ=255)
aCCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTc > 1:3102362/1‑69 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:3090683/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:2859321/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:2792538/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:2270698/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:1821746/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:1805044/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:1492275/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:1240980/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:638418/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:1149160/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:631676/53‑1 (MQ=255)
cacaATGGTGAGATGCGTTTCCCAACCGCGCGCAAGGGCTTCCGCATCggtag < 1:1467250/53‑1 (MQ=255)
acaATGGTGAGATGCGTTTCCCAACCGCGCGCGAGGGCTTCCGCATCggtag < 1:3133033/52‑1 (MQ=255)
gagaTGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCaa < 1:2330466/69‑1 (MQ=255)
gagaTGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCaa < 1:2363986/69‑1 (MQ=255)
gagaTGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCaa < 1:771917/69‑1 (MQ=255)
agaTGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCaa < 1:1934008/68‑1 (MQ=255)
gCGTTTCCCAACCGCGCGCGAGAGATTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAAcgc > 1:553015/1‑69 (MQ=255)
gCGTTTCCCAACCGCGCGCGAGAGATTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAAcgc > 1:1305088/1‑69 (MQ=255)
cGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAAcgcg > 1:2975921/1‑69 (MQ=255)
cGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAAcgcg > 1:2402004/1‑69 (MQ=255)
cGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAAcgcg > 1:2514087/1‑69 (MQ=255)
cGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCAAGCAAAAcgcg > 1:1754153/1‑69 (MQ=255)
cGTTTCACAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAAcgcg > 1:436649/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCaa > 1:1596982/1‑53 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:3289212/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:2343090/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:2561324/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:239176/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:2161233/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:1339605/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:1112347/1‑69 (MQ=255)
ccGCGCGCGAGGGCTTCCGCATCGGTAGTCAGTTTATCTACGGCTTCCAGCAAAACGCGCCCTCGTTcc > 1:156320/1‑69 (MQ=255)
gcgcgAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCcaaca < 1:1109580/69‑1 (MQ=255)
gcgcgAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCcaaca < 1:3357385/69‑1 (MQ=255)
gcgcgAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCcaaca < 1:1965769/69‑1 (MQ=255)
gcgcgAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCcaaca < 1:1667796/69‑1 (MQ=255)
gcgcgAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCcaaca < 1:654216/69‑1 (MQ=255)
cgcgAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCcaaca < 1:3168339/68‑1 (MQ=255)
|
AAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTGAGATGCGTTTCCCAACCGCGCGCGAGAGCTTCCGCATCAGTAGTCAGTTTATCTGCGGCTTCCAGCAAAACGCGCCCTCGCTCCAACA > minE/2089079‑2089208
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
