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 |
|
A4 F1 I2 R1
|
67 |
32.5 |
1435938 |
95.9% |
1377064 |
112.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,271,600 |
(C)5→6 |
coding (171/1146 nt) |
garK ← |
glycerate kinase I |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,271,595 | 1 | . | C | 94.4%
| 59.2
/ ‑3.0
| 18 | coding (176/1146 nt) | garK | glycerate kinase I |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (9/8); total (9/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
CGTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑CCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTGGC > NC_000913/3271460‑3271725
|
cgTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑ccc > 2:576654/1‑139 (MQ=255)
cgTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑ccc > 2:337786/1‑139 (MQ=255)
ccGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑ccc‑ccctggg < 1:312990/139‑6 (MQ=255)
aCCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCa > 2:256511/1‑139 (MQ=255)
cAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGc > 1:226991/1‑139 (MQ=255)
cTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCAcc < 1:258759/139‑1 (MQ=255)
ccgccATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCAcc < 2:124692/132‑1 (MQ=255)
ccgccATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCAcc > 1:124692/1‑132 (MQ=255)
ttttGCCATCGCCGGATATCCCCCAACGGGCATTCCCTTTCTCGCCCAGCGGCCCTGGAACCCAGGCGTGACGTTCAG‑CCCTCCTGGTTGGCTGCGATCATCGCTTCCTCCGTTCCTTCGCCACCGTCGGCAACCGGaa < 2:224934/139‑1 (MQ=255)
ttGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACa < 1:337786/139‑1 (MQ=255)
ccATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGaa < 2:18113/139‑1 (MQ=255)
gCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa > 1:495091/1‑129 (MQ=255)
gCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa < 2:495091/129‑1 (MQ=255)
cccccAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATc > 1:363025/1‑139 (MQ=255)
ttCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAAt < 2:363025/139‑1 (MQ=255)
cGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCtt > 2:369624/1‑139 (MQ=255)
tAACCCAGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTgcg < 1:174187/139‑1 (MQ=255)
aGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa < 2:206314/76‑1 (MQ=255)
aGGCGTGACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGaa > 1:206314/1‑76 (MQ=255)
gACGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTgg > 1:521231/1‑139 (MQ=255)
aCGTTCAGCCCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTGGc > 2:492990/1‑139 (MQ=255)
|
CGTTTTTCCGCAGGTACCAGCTCCAGCCCACTGGCCGCCGCCATTTCAATAAACGCGGTTTTGCCATCGCCGGAGATCCCCCAACTGGCATTCACTTTCTCGCCCAGCGGCCCTGTAACCCAGGCGTGACGTTCAG‑CCC‑CCTGGGTGGCTGCAATCATCGCTTCCACCGTTCCTTCGCCACCGTCGGCAACCGGAACAGAAACGTACTGTGCATCAGGAAAAATTTCCCGAAATCCTTTTTCTATCGCCTGCGCAACCTCGCTGGC > NC_000913/3271460‑3271725
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
