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 |
2,712,432 |
A→T |
68.4% |
G643G (GGT→GGA) |
nirB ← |
nitrite reductase, large subunit, NAD(P)H‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,712,432 | 0 | A | T | 68.4%
| 48.0
/ 23.4
| 44 | G643G (GGT→GGA) | nirB | nitrite reductase, large subunit, NAD(P)H‑binding |
| Reads supporting (aligned to +/- strand): ref base A (9/5); new base T (17/13); total (26/18) |
| Fisher's exact test for biased strand distribution p-value = 7.48e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAGCGGTTTTCCAGTTCCACGCCGAGGCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGACCGGTTTCGAA > minE/2712367‑2712488
|
tAGCGGTTTTCCAGTTCCACGCCGAGGCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTAc < 1:696043/67‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:1041210/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:2851369/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:3136592/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:2718543/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:2637051/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:2062797/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:1927063/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:1783643/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:1159786/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:927182/69‑1 (MQ=255)
gCCGAGGCCGACGCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:1181291/69‑1 (MQ=255)
ccGTGGCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGc < 1:842875/69‑1 (MQ=255)
ccGAGGCCGACTCTGTCGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:524899/68‑1 (MQ=255)
cGAGGCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGc < 1:2877928/68‑1 (MQ=255)
gCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGc > 1:1857981/1‑69 (MQ=255)
gCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGc > 1:1023224/1‑69 (MQ=255)
gCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGc > 1:2558784/1‑69 (MQ=255)
gCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGc > 1:1083186/1‑69 (MQ=255)
gCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGc > 1:1110409/1‑69 (MQ=255)
cTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCa < 1:2657465/69‑1 (MQ=255)
cGCCAACACCGTAGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACg < 1:1211559/52‑1 (MQ=255)
gCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGc > 1:779345/1‑69 (MQ=255)
gCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGc > 1:173782/1‑69 (MQ=255)
gCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGc > 1:2645583/1‑69 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAg > 1:588425/1‑43 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:917848/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:643032/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:973185/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:751139/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:3041705/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:2920031/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:2788279/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:257304/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:2529029/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:2525093/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:2450441/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:2121171/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:1889221/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:167923/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAcc > 1:1407981/1‑64 (MQ=255)
aGCGGCACCAGGTGCTTCCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGAc > 1:2355254/1‑63 (MQ=255)
gCACCAGGTGCTACCCACGCAGGTTTTTGCCATACGCAGTGCTTTCGCATAGGCATGACCGGTTTCGaa > 1:395823/1‑69 (MQ=255)
aGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCa < 1:1464023/44‑1 (MQ=255)
|
TAGCGGTTTTCCAGTTCCACGCCGAGGCCGACGCTGTCGCCAACGCCGTAGCGGCACCAGGTGCTACCCACGCAGGTTTTCGCCATACGCAGTGCTTTCGCATAGGCATGACCGGTTTCGAA > minE/2712367‑2712488
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
