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 F24 I1 R1
|
60 |
68.7 |
2919236 |
98.6% |
2878366 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,499,480 |
2 bp→AC |
intergenic (+57/‑106) |
trpS → / → zapE |
tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,499,480 | 0 | C | A | 92.9%
| 39.0
/ ‑6.1
| 14 | intergenic (+57/‑107) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (4/9); total (4/10) |
| 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 |
| * | NC_002947_CJ‑RC | 1,499,481 | 0 | A | C | 100.0%
| 43.8
/ NA
| 14 | intergenic (+58/‑106) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (4/10); total (4/10) |
GACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGTGTT‑TCGGG‑CACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTG > NC_002947_CJ‑RC/1499340‑1499619
||
gACGGGCCGCAGTTCGACACCGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCttt < 1:71302/149‑1 (MQ=255)
gACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACTGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCttt < 7:15712/149‑1 (MQ=255)
ggCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCg < 8:327552/149‑1 (MQ=255)
ccGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGgt < 7:17851/149‑1 (MQ=255)
ttCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGttcgc < 5:62936/149‑4 (MQ=255)
gACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGttcgcgg < 4:64844/148‑6 (MQ=255)
gACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGttcgcgg < 5:197364/148‑6 (MQ=255)
gAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCATGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGc < 5:237665/94‑1 (MQ=255)
gAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCATGCCCGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGc > 6:237665/1‑94 (MQ=255)
ccgcgggcggCCCCGCTAAACCGGCG‑CGGGGGGCCTGGCCCCGGGCTTTGCCTGTGTC‑CGGGGCCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATc < 2:227815/147‑1 (MQ=255)
ccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt > 6:165600/1‑147 (MQ=37)
gcgAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGG‑CCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGaa > 3:107464/1‑149 (MQ=37)
ccgcGGTGCATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGG‑CCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCa < 4:107464/149‑1 (MQ=37)
cATGGCACC‑GGCTTTGCCGGTGTTCGCGGG‑CACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTg > 5:78112/1‑148 (MQ=38)
||
GACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGTGTT‑TCGGG‑CACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTG > NC_002947_CJ‑RC/1499340‑1499619
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
