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 |
|
A4 F40 I1 R1
|
29 |
30.2 |
1007882 |
98.6% |
993771 |
143.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,296,381 |
+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 | 4,296,380 | 1 | . | C | 92.0%
| 61.0
/ 1.3
| 25 | intergenic (+586/+56) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (12/11); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 4.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 |
| * | NC_000913 | 4,296,380 | 2 | . | G | 92.0%
| 61.1
/ 1.4
| 25 | intergenic (+586/+56) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (12/11); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 4.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01 |
AACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTA‑‑C‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGC > NC_000913/4296284‑4296511
||
atcggcTGTTGCGCCGCTGAACGCGTCGTATCAGGCCTACGCGATTGTGTGTTATTGCCTGTTGTAGAGGGTTTTTGTAGTTAGGATAATTCGGTTTTG‑‑C‑‑CGCATCGGAGATCTTTGGCTGTTGCGACGCTTGCCGCGTCTTATCAGGc < 4:16604/144‑1 (MQ=2)
gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGAGGTAGCGTGAGTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCCTCCGACATCAATGCCGGATGCGACGCTTGCCGCGTCTTATCAGGCCTGTCTTAACCg > 4:111845/1‑149 (MQ=1)
aCGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGt > 6:86110/1‑149 (MQ=12)
cGCTTAACGCGTCTTATCAGGCCTTCGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATATGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTTCCGCGTCTTATCAGGCCTATCTTAACCGtt < 1:38426/149‑1 (MQ=11)
cGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGtt < 2:96677/149‑1 (MQ=12)
aaCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGtt > 5:14003/1‑148 (MQ=255)
aCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa > 8:22760/1‑149 (MQ=255)
aTCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa > 2:105792/1‑149 (MQ=255)
tCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAAc > 2:137254/1‑149 (MQ=255)
acTACTCCACACAGCGCAATAGCCTGATTTAGCGTGATGAGGTACGTCGGATAAGGCG‑‑CTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTc < 3:83468/148‑1 (MQ=17)
cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTcac < 7:22760/147‑1 (MQ=255)
cagacagaGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCg < 6:121578/149‑1 (MQ=255)
gACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGt < 2:106748/149‑1 (MQ=255)
tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt < 4:84703/124‑1 (MQ=255)
tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCtt > 3:84703/1‑124 (MQ=255)
gATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAAc > 7:58437/1‑99 (MQ=1)
gATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAAc < 8:58437/99‑1 (MQ=1)
aTTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa > 5:58277/1‑148 (MQ=255)
cGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCt > 7:99894/1‑147 (MQ=255)
gTAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAAc < 5:86110/148‑1 (MQ=255)
gTAGGTCGGATAAGGCG‑‑TTTA‑‑CGACTCATCCGACATCAATTCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAAc < 7:63737/148‑1 (MQ=37)
tAGGTCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAAc > 4:86587/1‑147 (MQ=255)
tCGGATAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGc < 1:43776/149‑1 (MQ=255)
aTAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCa < 1:32298/131‑1 (MQ=255)
aTAAGGCG‑‑TTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCa > 2:32298/1‑131 (MQ=255)
||
AACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑‑TTTA‑‑C‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGC > NC_000913/4296284‑4296511
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑C‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGCGCCTTTTGCT > NC_000913/4296297‑4296524
|
ACGCTTAACGCGTCTTATCAGGCCTTCGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATATGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTTCCGCGTCTTATCAGGCCTATCTTAACCGTTG < NB501016:228:HFK2FAFXY:1:11206:18950:17373/151‑1 (MQ=10)
TAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTA > NB501016:228:HFK2FAFXY:3:11409:17077:2210/1‑150 (MQ=22)
GACTACTCCACACAGCGCAATAGCCTGATTTAGCGTGATGAGGTACGTCGGATAAGGCGCTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCA < NB501016:228:HFK2FAFXY:2:21206:1521:1751/151‑1 (MQ=47)
ACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACA < NB501016:228:HFK2FAFXY:4:11502:22190:17767/149‑1 (MQ=60)
CTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTC > NB501016:228:HFK2FAFXY:2:21206:18109:16183/1‑126 (MQ=59)
TGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACC > NB501016:228:HFK2FAFXY:4:21402:9807:18703/1‑101 (MQ=4)
GATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATAC > NB501016:228:HFK2FAFXY:3:11608:21557:7422/1‑150 (MQ=60)
GCGTGATTTTGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTC > NB501016:228:HFK2FAFXY:4:21605:15676:17098/1‑149 (MQ=60)
TGTAGGTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACC < NB501016:228:HFK2FAFXY:3:21412:12410:3494/150‑1 (MQ=60)
TGTAGGTCGGATAAGGCGTTTA‑‑CGACTCATCCGACATCAATTCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACC < NB501016:228:HFK2FAFXY:4:21406:6008:4623/150‑1 (MQ=60)
GTCGGATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCA < NB501016:228:HFK2FAFXY:1:11209:8004:9905/151‑1 (MQ=60)
GATAAGGCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAG < NB501016:228:HFK2FAFXY:1:11203:20541:17155/133‑1 (MQ=60)
GCGTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACTCTTGCCGCGTCTTATCAGGCCTATCTTAACCGGTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGCGCCTTTTG < NB501016:228:HFK2FAFXY:2:21208:5956:1462/151‑1 (MQ=60)
GTTTACGC‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGCGCCTTTTGCT < NB501016:228:HFK2FAFXY:1:21203:6833:14222/151‑1 (MQ=60)
|
ACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTA‑‑C‑‑CGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGCGCCTTTTGCT > NC_000913/4296297‑4296524
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
