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 F1 I1 R1
|
17 |
44.3 |
2973330 |
95.1% |
2827636 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,202,303 |
+TG |
coding (257/825 nt) |
iclR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,202,299 | 1 | . | T | 86.4%
| 66.2
/ 5.0
| 22 | coding (261/825 nt) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base T (9/10); total (11/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01 |
| * | REL606 | 4,202,299 | 2 | . | G | 85.7%
| 65.4
/ 5.9
| 22 | coding (261/825 nt) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base G (9/9); total (11/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
AAATTGCGCAGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑TGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGC > REL606/4202225‑4202359
||
aaaTTGCGCAGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑t < 1:1198163/76‑1 (MQ=255)
ttGCGCAGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑tgtg < 2:197501/76‑1 (MQ=255)
tGCGCAGGATAGGGTGAACAATCGCTAACAAATTGCGNCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑tgtgt > 1:1444810/1‑75 (MQ=255)
tGCGCAGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGATAGTTGCTGCCGACCATAAAGGCA‑‑TGTgc > 1:226364/1‑76 (MQ=255)
gcgcAGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑tgtgtg < 1:1016618/76‑3 (MQ=255)
aGGATAGGGTGAACAATCTCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑TGTgtgcgcc < 2:811207/76‑4 (MQ=255)
aGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCAGCTGCCGACCATAAAGGCA‑‑TGTgtgcgcc > 2:324201/1‑73 (MQ=255)
aGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTg > 2:471280/1‑76 (MQ=255)
gTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGccc > 2:753997/1‑76 (MQ=255)
aCAATCGCTAACAACTTGCTGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATCTGTGCGCCGATTGCCCAATg < 1:73083/76‑1 (MQ=255)
aaTCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTc < 1:398202/76‑1 (MQ=255)
tCGCTAACAAATTATGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGGCGATTGGCCAATGTccc < 1:126014/76‑1 (MQ=255)
cGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCTCCGATTGCCCAATGTCCCa < 1:1260062/76‑1 (MQ=255)
cGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCa > 2:1179296/1‑76 (MQ=255)
aaCAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCCATGTCCCAGTTc > 2:843243/1‑76 (MQ=255)
cAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGc > 2:136110/1‑76 (MQ=255)
aCGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCt < 1:852807/76‑1 (MQ=255)
ctctGGAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACg > 1:419216/1‑76 (MQ=255)
ggAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACg < 1:1030683/76‑1 (MQ=255)
ggAGAAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACg > 1:1040026/1‑76 (MQ=255)
gaAAGCTGCTGCCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGaaa > 1:1161576/1‑76 (MQ=255)
gctgcCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCctgct < 1:478428/76‑1 (MQ=255)
ctgcCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCctgctg < 2:1001410/76‑1 (MQ=255)
ctgcCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCctgctg < 1:735103/76‑1 (MQ=255)
tgcCGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGt > 1:1034743/1‑76 (MQ=255)
cGACCATAAAGGCATGTGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACGTGACGCACGNAACCCTGCTGTTGc < 1:1188/76‑1 (MQ=255)
||
AAATTGCGCAGGATAGGGTGAACAATCGCTAACAAATTACGGCTCTGGAGAAAGCTGCTGCCGACCATAAAGGCA‑‑TGTGCGCCGATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGC > REL606/4202225‑4202359
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
