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 |
|
A21 F5 I0 R1
|
24 |
41.2 |
1474486 |
89.7% |
1322613 |
148.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
4,296,296:1 |
+CG |
100% |
intergenic (+586/+56) |
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 | 90.0%
| 37.3
/ 0.8
| 20 | intergenic (+586/+56) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (5/13); total (6/14) |
| Fisher's exact test for biased strand distribution p-value = 5.21e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.07e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | NC_000913_3_pae_tpiA | 4,296,296 | 2 | . | G | 90.0%
| 38.3
/ 0.6
| 20 | intergenic (+586/+56) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (5/13); total (6/14) |
| Fisher's exact test for biased strand distribution p-value = 5.21e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.80e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑A‑‑C‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGC > NC_000913_3_pae_tpiA/4296212‑4296430
||
gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCGGGCCTATCTTAACCg > 1:273059/1‑149 (MQ=255)
cgcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAt < 1:734247/149‑1 (MQ=255)
tCTTATCAGGGCGACGCCAGACAGCGCAATAGCCTGACTTAGCGTGATTTTGTAGGGCGGATAAGGCGTT‑T‑‑ACGC‑CCCCTCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAttttt < 2:558729/149‑1 (MQ=14)
aTCAGGCCTACGCCAGAGAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa < 1:162004/149‑1 (MQ=255)
gCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTAGGGTGCTTTGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt > 1:695713/1‑149 (MQ=17)
cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCacac < 1:670923/149‑1 (MQ=255)
ggaaTTGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa < 2:71602/147‑1 (MQ=18)
gcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa < 1:467432/149‑1 (MQ=255)
gcAATACCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGCT‑T‑‑ACGC‑CGCATCCCCCACCAATGCCTGATGCGACGCTTAACTCCAGTTGGCAGGTCTATCTAAGCCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa < 1:287392/149‑1 (MQ=12)
aaTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGATGGTTAATTCTTCAAACTCTTCACACCCGGTATCAAAcc > 1:569338/1‑149 (MQ=18)
aaTAGCCTGATTTAGCGTGATTAAATAGGGCGGGTGGGGTGTTGT‑‑G‑‑CTTGCTGCCCGCAGAAATGCATGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAAcc < 1:164550/149‑1 (MQ=19)
tAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCt < 1:214239/149‑1 (MQ=255)
gCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTc < 1:75549/149‑1 (MQ=255)
cTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACGCCCGGTATCAAACCCTTCCa > 1:144092/1‑149 (MQ=255)
tAGAGTGAGTTTGTAGGGTGGATAAGGCGTG‑T‑‑ACGC‑CGCATCCGAGATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTCTCAAACCCTTCCATACAGc < 2:622809/149‑1 (MQ=21)
cGTGATTTTGTAGGTCGGATAAGGCGTT‑TGCG‑‑C‑CGCATCCGACATCAATGCCTGCTGAGACACTTGCCGCTTCTTATCAGGCCTATCTTAACCGTTGGTTAATGTTTCAAACTCTTCACACCCGGGCTCAAACCCTTCCATACAACTCa > 1:620633/1‑149 (MQ=21)
gTGATTTTGTAGGGGGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAg < 2:532385/149‑1 (MQ=25)
gTGATTTTGTAAGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAg < 1:383625/149‑1 (MQ=255)
tGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACCTACTTTTGAGAAGCAAAGGTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAgg > 1:541651/1‑149 (MQ=25)
gATAAGGCGTT‑T‑‑ACGC‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAgc < 1:329418/149‑1 (MQ=255)
||
GACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTT‑T‑‑A‑‑C‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGC > NC_000913_3_pae_tpiA/4296212‑4296430
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
