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 |
|
A22 F64 I1 R1
|
18 |
58.3 |
2092080 |
92.1% |
1926805 |
145.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
4,296,297 |
+GC |
intergenic (+587/+55) |
gltP → / ← yjcO |
glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 4,296,296 | 1 | . | C | 92.5%
| 92.6
/ 2.6
| 42 | intergenic (+586/+56) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base C (18/19); total (21/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01 |
| * | NC_000913_3_pae_tpiA | 4,296,296 | 2 | . | G | 92.7%
| 98.6
/ 2.7
| 42 | intergenic (+586/+56) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base G (19/19); total (21/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01 |
AACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑A‑‑C‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGC > NC_000913_3_pae_tpiA/4296200‑4296430
||
aaCGCCTGATGCGACGCTTAACGAGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑A‑A‑‑CATC‑GTATCAGGCATATATGACTGGAGCGACGCCTCCCGAGTCTTATCTGGc > 1:139607/1‑149 (MQ=11)
gCGACGCTTAGCGCGTCTTCTCAGGCCTACGCCAGACTGCCCATTAGTCTCATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGAAATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAAc < 1:605935/149‑1 (MQ=1)
cGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGtt > 2:880457/1‑149 (MQ=255)
aCGCGTTTTATCTGGCCTACGCCAGACATCGCAATTGCTTGATTTGGCGTGCATTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑TCATCTGACATCAATGCTTGATGCGTCGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa < 2:53939/149‑1 (MQ=11)
aCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGttca > 2:412873/1‑147 (MQ=255)
aCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa > 1:597251/1‑149 (MQ=255)
cgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAttt < 1:603319/149‑1 (MQ=255)
cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc < 1:361027/149‑1 (MQ=255)
aTCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGATCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCGTGCTGCGACGCTGTCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCtaa > 2:112520/1‑149 (MQ=14)
tCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCTCGTCTTATCATGCCTATCTTAACCGATAGTTAATTTTTCCAAc > 1:175693/1‑149 (MQ=14)
tCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCacat > 1:386286/1‑146 (MQ=255)
gCCTACGCCAGACAGCGCAATAGCCTGATTTAGTGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt < 1:787210/149‑1 (MQ=255)
gCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt < 1:787223/149‑1 (MQ=255)
gCCTACGCCAGACAGCGCAATAGCCTGATATAGCGTGATTTTGTAGGTCGAATAGGGAGTT‑T‑ACGC‑‑C‑GCCGCCGACATCAATGCCTGCTGCGACGCTTGCCGCACCTTATCAGGCCTATCTTAACTGTGGGTTAATATTTCAAAGTCtt > 1:882580/1‑149 (MQ=14)
cTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTca < 1:340061/149‑1 (MQ=255)
cTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑A‑‑CG‑CGGCATCCGACATCAATGCCTGATAAGCCGCTTCCCGCGTCTTAACAGGCCTATCTTAACCGCTTGTTCATTTTTCATACTCTTca > 2:58704/1‑149 (MQ=14)
gCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc > 2:223202/1‑149 (MQ=255)
cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGAATCaa > 1:173798/1‑149 (MQ=255)
cgcAATAGCCTGACTTCGCGTGATATAACTTGCCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCCGTCTCaa > 2:749201/1‑149 (MQ=17)
gaaaTAGCCTGATTTAGCGTGATTTTTTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa < 2:209422/147‑1 (MQ=18)
aatatgcTGTTTTAGCGTGATTTTGTAGGTCGGATAAGGCCTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAAcc < 1:414028/143‑1 (MQ=18)
aaTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAAcc < 2:645119/149‑1 (MQ=255)
aaTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGACTCTCCTAACTGTTGGTTACATCTTCAAACTCTTCACACCCGGTATCAAAcc > 1:923074/1‑149 (MQ=17)
tAGCCTGATTCAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GGACCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCt < 2:1019658/149‑1 (MQ=18)
attcTGAGTTAGCGTGATTGTGTCGGTCGGATAAGGCGTC‑T‑ACGC‑‑C‑GCCTGCGCCATCAATGTCTGATGCGACGCTTGCCGCGTCTTATCAGGCATATCTTAACCGTGGGTTAATTTTTCAAACTCGTCACACCCGGTATCAAACCCtt < 2:561276/146‑1 (MQ=18)
aGCCTGATTTAGCGTGATTTTGTATGTCGGATAAGGCATT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCtt < 1:264369/149‑1 (MQ=21)
aGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCtt < 1:813161/149‑1 (MQ=255)
ggcTGATTTTCTGTGATGTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTc < 2:462528/147‑1 (MQ=21)
gCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTAACCCCCGGTATCAAACCCTTc > 2:295694/1‑149 (MQ=18)
ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ATGC‑‑C‑GCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc > 2:388800/1‑149 (MQ=255)
gATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa < 1:141720/149‑1 (MQ=255)
tttAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACACTTCCATACa > 2:388618/1‑149 (MQ=255)
cGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACCCCCGGTATCCAACCCTTCCATACACCTCa > 2:504984/1‑149 (MQ=21)
tGATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCTGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAgg > 2:992316/1‑149 (MQ=255)
gATTTTGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCATTACATACAGCTCAGGt > 2:135243/1‑149 (MQ=21)
ttttGTAGGTCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTCAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTc < 1:880457/149‑1 (MQ=255)
tAGGTCGGATAAGGCGTT‑T‑ATGC‑‑C‑GCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCa < 1:388800/149‑1 (MQ=255)
ggTCGGATATGGCGTTGTCG‑‑C‑‑C‑GCTTCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGt < 2:296222/149‑1 (MQ=37)
gTCGGATAAGGCGTT‑A‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCAATACAGCTCCGGTTCAACCAGTg > 1:785318/1‑149 (MQ=25)
tCGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACACTGGCCTTGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACATCTCAGGTTCAACCAGTGc > 1:464419/1‑149 (MQ=37)
cGGATAAGGCGTT‑T‑ACGC‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGTGTTTTGCGGTGGCGATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCa < 1:502016/149‑1 (MQ=25)
taTAAGGCGTT‑T‑ACTC‑‑C‑TCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAgc < 1:489509/148‑1 (MQ=255)
||
AACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑A‑‑C‑‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGC > NC_000913_3_pae_tpiA/4296200‑4296430
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
