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 |
|
A13 F69 I0 R1
|
1426 |
148.0 |
5875178 |
97.4% |
5722423 |
123.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
2,090,124 |
C→G |
47.7% |
intergenic (+78/‑68) |
hisL → / → hisG |
his operon leader peptide/ATP phosphoribosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,090,124 | 0 | C | G | 47.7%
| 3.6
/ 72.8
| 44 | intergenic (+78/‑68) | hisL/hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| Reads supporting (aligned to +/- strand): ref base C (11/12); new base G (11/10); total (22/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.99e-02 |
CAGAGACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGAC > NC_000913/2089985‑2090251
|
caGAGACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgg < 4:265746/149‑1 (MQ=255)
gagaCTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGCAATAAAAAAGCCCCCGGAAGGTGATCTTCCggg < 4:303350/149‑1 (MQ=38)
gagaCTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGCAATAAAAAAGCCCCCGGAAGGTGATCTTCCggg > 3:303350/1‑149 (MQ=38)
ttttATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgggg < 4:809084/144‑1 (MQ=255)
ttttATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgggg > 3:809084/1‑144 (MQ=255)
acacGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgg > 4:45680/1‑135 (MQ=255)
acacGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgg < 3:45680/135‑1 (MQ=255)
acGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCa < 4:555076/125‑1 (MQ=255)
acGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCa > 3:555076/1‑125 (MQ=255)
aaTTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg < 1:1241636/126‑1 (MQ=255)
aaTTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg > 2:1241636/1‑126 (MQ=255)
aTTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgggg > 2:606690/1‑126 (MQ=255)
aTTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgggg < 1:606690/126‑1 (MQ=255)
tttAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCa < 3:1421143/115‑1 (MQ=255)
tttAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCa > 4:1421143/1‑115 (MQ=255)
aaaCACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgggg < 3:688724/122‑1 (MQ=255)
aaaCACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgggg > 4:688724/1‑122 (MQ=255)
tcaccatcatcCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCAc < 4:211098/99‑1 (MQ=255)
tcaccatcatcCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCAc > 3:211098/1‑99 (MQ=255)
catcatcCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgg > 4:600357/1‑102 (MQ=255)
catcatcCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgg < 3:600357/102‑1 (MQ=255)
gTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg < 1:466623/89‑1 (MQ=38)
gTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg > 2:466623/1‑89 (MQ=38)
tCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg < 2:832792/88‑1 (MQ=38)
tCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg > 1:832792/1‑88 (MQ=38)
gAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgggg > 3:238253/1‑68 (MQ=255)
gAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCgggg < 4:238253/68‑1 (MQ=255)
ccccGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAagag > 1:1229478/1‑69 (MQ=255)
ccccGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAagag < 2:1229478/69‑1 (MQ=255)
cccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACg < 2:583584/101‑1 (MQ=39)
cccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACg > 1:583584/1‑101 (MQ=255)
cccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGAc < 4:200259/138‑1 (MQ=255)
cccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGAc > 3:200259/1‑138 (MQ=255)
ccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGTTTCAGTCAGGTTTAACGAGGAATAACAAAATga > 1:1159264/1‑81 (MQ=37)
ccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATga < 2:1159264/81‑1 (MQ=38)
ccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTAc > 1:506763/1‑99 (MQ=39)
ccGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATga < 4:1187313/81‑1 (MQ=255)
ccGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATga > 3:1187313/1‑81 (MQ=255)
ccGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTa < 3:42237/98‑1 (MQ=255)
ccGGAAGATCACCTGCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTa > 4:42237/1‑98 (MQ=255)
gATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGtgatga > 2:178176/1‑130 (MQ=255)
gATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGtgatga < 1:178176/130‑1 (MQ=255)
aTCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATaa > 2:1284005/1‑66 (MQ=255)
aTCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATaa < 1:1284005/66‑1 (MQ=255)
|
CAGAGACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGAC > NC_000913/2089985‑2090251
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
