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 F31 I1 R1
|
56 |
85.7 |
3650428 |
98.3% |
3588370 |
146.6 |
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 | 92.9%
| 27.1
/ ‑3.9
| 15 | 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 (7/6); minor base C (0/1); total (7/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 93.3%
| 45.0
/ ‑2.9
| 15 | 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 (7/7); total (7/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 93.3%
| 45.0
/ ‑2.9
| 15 | 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 (7/7); total (7/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01 |
TGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558279‑5558551
|||
tGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccc > 3:211431/1‑145 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccccg < 8:109089/149‑7 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccccg > 7:109089/1‑143 (MQ=255)
cAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTc > 7:177935/1‑149 (MQ=255)
aaTTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGCATACCAACACCGCTCAGGTGGGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCgt < 8:58249/149‑1 (MQ=38)
ggCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGcaaca < 4:211431/149‑1 (MQ=255)
gCCGGGGCAGTGATTAGTCGGGCGCAAATGAGCAACTCTTTTTGTAATGTGTCGCCTACATCATAGCAACACCGCTCCGGTGTGGTAGCGTCCTTGTGTCGCTAACGGGCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGcaacaa < 2:262267/149‑1 (MQ=255)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcgg > 3:64955/1‑106 (MQ=255)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcgg < 4:64955/107‑2 (MQ=255)
cATGAGCAACTCGTTTTGTCTTGTGGCGCCGACAGCATAGCAACCCCGCTCTGGTGTGGGAGCGGCGTGGTGTCGCTAACGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc < 8:177935/149‑1 (MQ=255)
aGCAACTCCTTTTGCCATGGGGCGCCGACAGCATACCAACACCGCTCAGGGGTGGGAGCGGCCTTGTGCCGCTAAAGGGCCCCAT‑‑‑CGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 5:230426/149‑1 (MQ=255)
gCAACTCCTTTTGTCTTGTGTCGCCTACAGCATACCAACACCGCTCTGGTGTGGGCGCGGCGTTGTGTCGCTAACGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGac < 2:168256/149‑1 (MQ=255)
cAGCATAGCAACACCGCTCTGGTGTGGGTGCGGCCTTGTGTCGCTAATGGCCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGc < 6:412583/149‑1 (MQ=37)
ggggAGCGCCCTTGGGCCGCTAACGGGCCGCATCCCGGCC‑‑‑CCGCCAATTTCCGCGTGTATCCAACAAACCTGGGGCTGCTATGCAGCCCTTGCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGc < 8:371065/148‑1 (MQ=255)
cTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAg > 8:369385/1‑149 (MQ=255)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTgcgc > 1:122621/1‑149 (MQ=38)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 8:22651/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 8:293585/1‑149 (MQ=255)
cgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTGCGCGTGTATGCAAAAAACCAGGGGCAGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCACGCATCAGGCCCGGAACAGCCCCCCGCTGGCGCGCAGCTGAgccgc > 3:73287/1‑149 (MQ=37)
cgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:364728/1‑149 (MQ=255)
|||
TGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558279‑5558551
|
| 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
N/A
