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 |
2,260,039 |
G→A |
50.8% |
R368R (CGC→CGT) |
rpoB ← |
RNA polymerase, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,260,039 | 0 | G | A | 50.8%
| ‑6.1
/ 53.3
| 59 | R368R (CGC→CGT) | rpoB | RNA polymerase, beta subunit |
| Reads supporting (aligned to +/- strand): ref base G (16/13); new base A (20/10); total (36/23) |
| Fisher's exact test for biased strand distribution p-value = 4.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAACAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAGAGATA > minE/2259976‑2260105
|
gaaCAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGc > 1:2227870/1‑65 (MQ=255)
gaaCAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTa < 1:3164050/69‑1 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGa > 1:459819/1‑68 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGa > 1:2582479/1‑68 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGa > 1:1769573/1‑68 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGa > 1:2707047/1‑68 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGa > 1:639866/1‑68 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGAt > 1:1536893/1‑69 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGAt > 1:1137833/1‑69 (MQ=255)
cAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGCAGa > 1:1037959/1‑68 (MQ=255)
ttCTCGCACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:442851/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTc > 1:2842381/1‑68 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:391860/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:366736/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:3313803/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:424231/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:3146784/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:299673/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:433953/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:2634778/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:2469589/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:245250/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:2061732/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:1041047/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:1130945/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:1298044/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:1810100/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:1470974/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:906262/1‑69 (MQ=255)
ttCTCGAACAGGCTTTCAGCAGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCt > 1:163709/1‑69 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTTGTTa > 1:1246635/1‑69 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGt > 1:1909613/1‑67 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTa > 1:1691832/1‑69 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTa > 1:176384/1‑69 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTa > 1:2917584/1‑69 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTa > 1:770991/1‑69 (MQ=255)
tCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTa > 1:1272660/1‑69 (MQ=255)
cGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAg < 1:1500509/67‑1 (MQ=255)
cGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAg < 1:486709/67‑1 (MQ=255)
cGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAg < 1:309936/67‑1 (MQ=255)
cGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAg < 1:950780/67‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTGGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:1495335/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:955985/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:815804/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:812690/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:80594/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:964006/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:2633935/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:2441675/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:1469825/69‑1 (MQ=255)
aGTCGGCGGCTCGCCAGGGCGCATCATACGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTgg < 1:1044994/69‑1 (MQ=255)
ggCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGttt < 1:155981/69‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAgaga < 1:3007439/67‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAgaga < 1:599306/67‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAgaga < 1:2795252/67‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAgaga < 1:713747/67‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAGAGata < 1:1871498/69‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAGAGata < 1:183565/69‑1 (MQ=255)
atGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAGAGata < 1:1364898/69‑1 (MQ=255)
|
GAACAGGTTCTCGAACAGGCTTTCAGCTGCTTCACGAGTCGGCGGCTCGCCAGGGCGCATCATGCGGTAGATTTCTACCAGTGCGCTCAGACGGTCGTTAGTTGGGTCGACACGTAAGGTTTCAGAGATA > minE/2259976‑2260105
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
