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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
306,800 |
G→A |
24.4% |
A96V (GCT→GTT) |
ylaB ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 306,800 | 0 | G | A | 24.4%
| 83.5
/ 19.5
| 65 | A96V (GCT→GTT) | ylaB | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (23/26); new base A (10/6); total (33/32) |
| Fisher's exact test for biased strand distribution p-value = 3.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.06e-01 |
GGAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACA > minE/306735‑306867
|
ggAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGcc < 1:1698369/68‑1 (MQ=255)
ggAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGcc < 1:2082554/68‑1 (MQ=255)
ggAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGc < 1:846281/67‑1 (MQ=255)
ggAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGc < 1:1920236/67‑1 (MQ=255)
ggAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGc < 1:2845423/67‑1 (MQ=255)
aaGGTATCGGGCGGACTTTGATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACt < 1:3263159/69‑1 (MQ=255)
gCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAatat < 1:732403/69‑1 (MQ=255)
gCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAatat < 1:2263538/69‑1 (MQ=255)
gCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAatat < 1:1554417/69‑1 (MQ=255)
ggcTTTCATGCTCCAGAGACGAACAGTGGGGAACGTTGTTATCGATATAAACCACTTCCTGAATATAGc < 1:673839/67‑1 (MQ=255)
ggcTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAACCACTTCCTGAATATAGc < 1:2101109/67‑1 (MQ=255)
ggcTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAACCACTTCCTGAATATAGc < 1:22994/67‑1 (MQ=255)
ggcTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAACCACTTCCTGAATATAGc < 1:2756156/67‑1 (MQ=255)
ggcTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAACCACTTCCTGAATATAGc < 1:3248311/67‑1 (MQ=255)
ggcTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAACCACTTCCTGAATATAGc < 1:1110350/67‑1 (MQ=255)
tttCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGAt < 1:1370129/69‑1 (MQ=255)
tttCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGAt < 1:2856542/69‑1 (MQ=255)
tttCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGAt < 1:1165825/69‑1 (MQ=255)
tttCATGATCCAGAGACGAAAACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGAt < 1:3008104/69‑1 (MQ=255)
ccAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg < 1:1930664/69‑1 (MQ=255)
ccAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg < 1:1981117/69‑1 (MQ=255)
ccAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg < 1:2103386/69‑1 (MQ=255)
ccAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg < 1:2255292/69‑1 (MQ=255)
ccAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg < 1:2553157/69‑1 (MQ=255)
cAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg < 1:1648207/68‑1 (MQ=255)
gagaCGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATa < 1:910447/69‑1 (MQ=255)
gagaCGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATa < 1:165472/69‑1 (MQ=255)
gagaCGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATa < 1:1482842/69‑1 (MQ=255)
gaCGAACACTGGGGAACGTTGTTATCGATATAAGCCAc > 1:3082263/1‑38 (MQ=255)
gaCGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATa > 1:1478199/1‑67 (MQ=255)
gaCGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATAc > 1:1140969/1‑68 (MQ=255)
gaCGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATAc > 1:3260097/1‑68 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTct > 1:632678/1‑68 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:1262746/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:1021453/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:289863/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:2848459/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:2802605/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:2661820/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:2370585/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTcc > 1:16530/1‑69 (MQ=255)
ggAACGTTGTTATCGATATAAACCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTc > 1:528721/1‑68 (MQ=255)
cGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTc > 1:108380/1‑64 (MQ=255)
cGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATga < 1:1215491/69‑1 (MQ=255)
cGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATga < 1:1862731/69‑1 (MQ=255)
cGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATga < 1:3415196/69‑1 (MQ=255)
gATATAAGCCACTTCCTGAATATAGCGATAACTGTAAg > 1:3383295/1‑38 (MQ=255)
gATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATAccc > 1:1705991/1‑44 (MQ=255)
gATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCTACGCATTTcc > 1:3420184/1‑55 (MQ=255)
gATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTc > 1:1807227/1‑69 (MQ=255)
gATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTc > 1:1418013/1‑69 (MQ=255)
taAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGc > 1:2678289/1‑67 (MQ=255)
taAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGc > 1:2457774/1‑67 (MQ=255)
taAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGc > 1:1176063/1‑67 (MQ=255)
taAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTa < 1:1654475/69‑1 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATAccc > 1:288430/1‑38 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:3317308/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:2128568/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:1948966/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:2484331/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:3176534/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:3093188/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:1164521/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:2229009/1‑69 (MQ=255)
aGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACa > 1:1235184/1‑69 (MQ=255)
|
GGAAGGTATCGGGCGGACTTTCATGCTCCAGAGACGAACACTGGGGAACGTTGTTATCGATATAAGCCACTTCCTGAATATAGCGATAACTGTAAGATACCCGACGCATTTCCATGAGATGGGCTTCGCTACA > minE/306735‑306867
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
