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 |
|
A3 F14 I1 R1
|
57 |
86.1 |
3667460 |
98.7% |
3619783 |
146.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 88.9%
| 14.8
/ ‑5.5
| 10 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); major base G (2/6); minor base C (0/1); total (2/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 90.0%
| 27.0
/ ‑2.8
| 10 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (2/7); total (2/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 90.0%
| 26.9
/ ‑2.8
| 10 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (2/7); total (2/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
CACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCA > NC_002947_CJ‑RC/5558282‑5558541
|||
cACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcggccc < 7:365931/146‑5 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑gcggccccgg > 1:388447/1‑141 (MQ=255)
gggCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCt > 3:374762/1‑149 (MQ=255)
gctgttaTTTGTGGGGCGTACTTGATAAACTCTTTTTGTTTTGTGTGGCGTACAGAATAGCAACACGGCTCTGGTGTGGGTGGGGCTTTGTGTCGCTAATGGGCCTAATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 4:374762/143‑1 (MQ=255)
gctgctaTTAGTGGGGCGGAAATGAGCAACTCCTTTTGTCATGTGTCCCCTACAGCTTAGCAACACCGCGCTGGTGTGGTTGCGGCTTTGTGGGGCTAAAGGGCCGAATAGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 2:338382/143‑1 (MQ=255)
gCAGCGATTAGTCGGGCGTACATGACCAACTCGTTTTGTCTTGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 8:70606/148‑1 (MQ=37)
gCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 6:241983/149‑1 (MQ=255)
tCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGc < 2:388447/149‑1 (MQ=255)
aGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgcg < 2:72036/148‑1 (MQ=38)
aaCTCATTTTGTCATGTGCCCCCCACAGCATACCAACCCCCCTCCGGGGTGGGCGCGGCCTTGGGCCGCTAACGGCCCCCATA‑‑‑GCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGacac < 4:146066/149‑1 (MQ=255)
ggttggggCCTTGGGCGGCTAAGGGGCCGCATC‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCt < 5:454155/143‑1 (MQ=255)
ccTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTACGCGGGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGCCACAAGGCCCCCAAAGGACCGCGCACGCGTCCGGCCCGGAACTGGCCCAGGCAGgcgcgcc > 1:289371/1‑148 (MQ=25)
|||
CACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCA > NC_002947_CJ‑RC/5558282‑5558541
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
