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 F14 I0 R1
|
248 |
61.6 |
2601574 |
98.7% |
2567753 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
3,152,278 |
G→C |
34.5% |
A145P (GCA→CCA) |
PP_2768 → |
branched‑chain amino acid ABC transporter permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 3,152,278 | 0 | G | C | 34.5%
| 22.8
/ 3.1
| 20 | A145P (GCA→CCA) | PP_2768 | branched‑chain amino acid ABC transporter permease |
| Reads supporting (aligned to +/- strand): ref base G (7/6); new base C (3/4); total (10/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAC‑GGCGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCTGCGTGCGGTGGCCGACGATCCCCGCGCGGCGATGAGCGTCGGTATCCGCCTGCCGAGGGTGTGGGCGGTGGTCTGG > NC_002947_CJ‑RC/3152134‑3152421
|
gCCACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAc < 8:281206/149‑1 (MQ=255)
cACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGCCCTGTTCGCCCCCCCacccg > 7:140807/1‑145 (MQ=255)
cACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAc‑gg < 2:179130/149‑1 (MQ=255)
gCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAc‑ggcgg < 6:293930/149‑1 (MQ=255)
gCTCGGCCTGGCCTACATCATCGAGGGCGCAGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCCCAAc‑cgcgg > 7:9708/1‑149 (MQ=255)
tCGGCCTGGGCTTCATCTTCGAGGTCGCCGCGCAGGCCTTATGGGGCGCACAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGACCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCATc‑ggcggcg < 2:311588/149‑1 (MQ=255)
gcctACATCTTCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCCAC‑GGGGGCGGGCCtggt > 7:238141/1‑149 (MQ=255)
ctACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAC‑GGCGGCGGCCCtggggg > 8:167672/1‑149 (MQ=255)
atcatcGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCCCCCCCAA‑CGCGGGGGCCCCGgtggtggg > 7:56947/1‑147 (MQ=255)
atggcgggCGCCGCCCAGGCCTTAGGGGGGGCCCAGGTTCACGGCCTGGTGCTGGCCATCAGCGACGCCCGGCTGGAGCTGGGGGGCGTGCTGCTGTCGCTGTTCGACCTTTTCGCCGCCGCAAG‑GGGGGCGGCCCTGGTGGTGCTTCt < 6:244854/144‑1 (MQ=255)
cgggCGCCGCCCTGGCCTTTTGGGGCGCCCCGGTTCCCGGCCTGTCGGGGGCCATCCGCGACGCCCCGGGGTCGGTGGGGGGCCGGGTGCGGTGGCTGTGCGCCCTGTCCGCCGCCCCACC‑GGGGGCGGCCCTGGTGGTGCTTCTGTcc < 8:238141/148‑1 (MQ=255)
ttATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCCCCGCAAC‑CGCGGCGGCCCGGGTGGGGGGTATGTCCATGCTGTTaaaaccccc > 6:259198/1‑143 (MQ=255)
aTGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAC‑GGCGGCGGCCCGGGTGGTGCTTCTGGCGGTGCTGTTCAAccgcccgc > 2:258234/1‑149 (MQ=255)
tGGGGCGCCCTGGTACACGGCTTGGCGCGGGCAATCTGCCCCCCCCCGTTGTTGCGGGGGGGCCGGCGGGTTGCGCAGTGCCCCCT‑TTCCGCGCCCCAACGGGGGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCAcgc < 6:221214/148‑1 (MQ=255)
cGGCCGGGCGGTGGCCATCCGCGACGCCCCGGTGGCGCGGGGGGGCGTGGTGGTGTCGCTGTTCGACGTGTCCGCCGCCCCACG‑GGGGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCtgc < 6:244070/149‑1 (MQ=255)
gCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAC‑GGCGGCGGCCCAGGTGGTGCTTCTGTCCTTGCTGTTAAACCGCACGCGCATCAGCCTGGCGCTGCGTGCGGTGGCcga > 2:321192/1‑149 (MQ=255)
gtcgggggggggCCGGCTGGTGGCGCTTTGCCACGTGTTCGCCCCCCAACC‑GGGGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCTGCGTGCGGTGGCCGACGATCCCCGCGCGGCGATGa < 8:220150/143‑1 (MQ=25)
gggggggCCTGGTGCTGTCGCTGTTCGACTTGGTGGCCGCGGCAAG‑GGGGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCTGCGTGCGGTGGCCGACGATCCCCGCGCGGCGATGAGCGTc < 8:140807/148‑1 (MQ=255)
gCAGTTCGACCTGTTCGCCCCCGCCAA‑CGCGGCGGCCCAGGTTGTGCGTCAGGCCATGGTGGTAAAACGCCCGCGCCTAGGGCGGGCGCAGCGTGCGGGGGCACCCCCACCCCCCCCGGCGAAGCGCGTCGGTATCCGCCTGCCGCggg > 2:247284/1‑149 (MQ=255)
cTGTTCGCCGCCGCAAC‑GGCGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCTGCGTGCGGTGGCCGACGATCCCCGCGCGGCGATGAGCGTCGGTATCCGCCTGCCGAGGGTGTGGGCggt > 6:151152/1‑149 (MQ=255)
ccgccgcAAC‑GGCGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCTGCGTGCGGTGGCCGACGATCCCCGCGCGGCGATGAGCGCCGGTATCCGCCTGCCGAGGGTGTGGGCGGTGGTCTgg > 5:16501/1‑149 (MQ=255)
|
GCCACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGCCTTATGGGGCGCCCAGGTTCACGGCCTGGAGCTGGCCATCAGCGACGCCCCGCTGGAGCTGGGCGGCCTGCTGCTGTCGCAGTTCGACCTGTTCGCCGCCGCAAC‑GGCGGCGGCCCTGGTGGTGCTTCTGTCCTTGCTGTTCAACCGCACGCGCATCGGCCTGGCGCTGCGTGCGGTGGCCGACGATCCCCGCGCGGCGATGAGCGTCGGTATCCGCCTGCCGAGGGTGTGGGCGGTGGTCTGG > NC_002947_CJ‑RC/3152134‑3152421
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
