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
A1 F9 I0 R1 71 67.1 1514203 90.7% 1373382 220.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,149,901 G→C 46.2% A362G (GCG→GGG)  yegI ← protein kinase‑related putative non‑specific DNA‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,149,9010GC46.2% 1.9 / 3.7 17A362G (GCG→GGG) yegIprotein kinase‑related putative non‑specific DNA‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (5/4);  new base C (2/6);  total (7/10)
Fisher's exact test for biased strand distribution p-value = 3.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCAGACTGCCAATAATCCAGATAGCCGCCAGCACAGGAACCAAAATAATATAACGCGGTTCTGCCTGAAGGCCGCAAAGCAGCAGCGATAATGCTGACAGTGCGATCTCAA‑GCAGAATGATGTATTCGCGCCGTAACAGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGTGCTACTGACGCCATCACCA‑TCGCCCAGACTTTCGCCAGCACAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTAGAGAGTCCAGTGCCGCTACCCACGCTTTAGCCGTCGGACGCCCGGTTG  >  NC_000913/2149685‑2150129
                                                                                                                                                                                                                          |                                                                                                                                                                                                                                       
gTCAGACTGCCAATAATCCAGATAGCCGCCAGCACAGGAACCAAAATAATATAACGCGGTTCTGCCTGAAGGCCGCAAAGCAGCAGCGATAATGCTGACAGTGCGATCTCAA‑GCAGAATGATGTATTCGCGCCGTAACAGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGTGCTACTAACGCCATCACCA‑tt                                                                                                                                                                                                                             >  1:156401/1‑227 (MQ=255)
   aacctcacAATAACCCAGATAGCCCCCAGCACAGGAACCAAAATAATATAACGCGGTTCTGCCTGAAGGCCGCAAAGCAGCAGCGATAATGCTGACAGTGCGATCTCAA‑GCAGAATGATGTATTCGCGCCGTAACAGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGTGCTACTGACGCCATCACCA‑TCGccc                                                                                                                                                                                                                         <  2:456826/222‑1 (MQ=255)
     aCTGCCAATAATCCAGATAGCCGCCAGCACAGGAACCAAAATAATATAACGCGGTTCTGCCTGAAGGCCGCAAAGCAGCAGCGATAATGCTGACAGTGCGATCTCAA‑GCAGAATGATGTATTCGCGCCGTAACAGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGGGCTACTTGCGCCCTCACCA‑TCGCCCa                                                                                                                                                                                                                        >  1:431160/1‑228 (MQ=255)
                 ccAGATCCCCGCATGCCCGGGAACAAAAATAAAATTACGCTGTTTCGCCTGGAGGGCACAAGGCGGGTGCGATAAGGTTGACAGTGCGGTCCCAA‑GCAGAGTGAGTTATTCGCGCCGTAACGGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGGGCTACTGACGCCATCACCA‑TCGCCCAGACTTTCGCCAGc                                                                                                                                                                                                           <  2:379741/229‑1 (MQ=255)
                                               attataACGCGTTTCTGCTAGAGGGCACAAACGCAGACGGGAAAATGGTGAC‑GTGGGATCTCAAGGCAAAATGATTTTTTGGGCCCGAAACAGGCTAAAGGGAAGCGGCCCGCCGGTCGGTTGGAAAGGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGTGCTACGGCCGCCATCCCCA‑TCGCCCAGACTTTCGCAAGCACAAAATTCCCGCCGGTGGTAATGACct                                                                                                                                                                               <  2:156401/225‑1 (MQ=255)
                                                      cgcgGTTCTGCCTGAAGGCCGCAAAGCAGCAGCGATAATGCTGACAGTGCGATCTCAA‑GCAGAATGATGTATTCGCGCCGTAACAGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGTGCTACTGACGCCAT‑ACCACTGGCCCAGACTTTTGCCCGCGCAAAATTTCCGCCGCGGGGAAGGACCCCTTCTcccg                                                                                                                                                                      >  1:254262/1‑227 (MQ=255)
                                                                                                                                        aaCAGTCCTAAAGGAGGCGGCCTGCCAGTCGGTTGGAAATGATCTGTTAATGGCAGTTGC‑AAGGCTGGGGGTCCTCCCAAGGCCATCACCA‑TCCCCCAGACTTACCCCAGCAAAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTg                                                                                   <  1:622703/229‑1 (MQ=255)
                                                                                                                                                       aGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGAGCTACCGCCCCCATAAACA‑CCCACCAAGCCTTTTCCAGCCCAAAAATCCCCCCCGGGGGAAAGACCTCTCCCCCCTGATTCAC‑AAAAAAAACAACACACTGATTTTCCACGACCAAACCGCGGGCAGCCAGCAAAAGGAG‑GGGGAAAACAtatagtgcgtaaaagaaaaaat                                                                    >  2:510119/1‑208 (MQ=255)
                                                                                                                                                            ccTGCCAGACGGTTGGAAATGATCGGGTAATGGCAGTTGA‑AATGCTGGCGGTGCTCCTTACGCCATCACCA‑ACCCCCAGAATTTCGCCCACACAAAATTTCCGCCGGGGGGAATTACCCCTTCTCCGGGGCCAATAAAAAAACAAAACACTTTG‑TTTTCCC‑GGGCCCACCCCAGGCAGGCAGTTAAAATGGCCGGGGAAAAAAGCCTTGCGCAAAAAACAAATTTCttt                                                               >  2:185406/1‑229 (MQ=255)
                                                                                                                                                                   gtggggttgAAATGGTCGGGTAATGGCAGTTGC‑AAGGGGGGGGGTGCACGCGGCCCCATCCCCC‑TCGCCCGGACTGTCCCCAGCAAAAAATTCCCGCCGGTGGTAATGACCTCTGCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTAGCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTg                                                          <  2:77847/219‑1 (MQ=255)
                                                                                                                                                                           gAAATGATCGGGTAATGGCA‑TTGCAAATGCTGGCGGTGTTACTGACCCCATCCCCA‑TCGCCCAGACTTCCGCCAGCACAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTaga                                                <  1:632520/229‑1 (MQ=255)
                                                                                                                                                                              agggttgtgttggggCAGGTGC‑AATGCTGGCGGTGCTACCTACCACATCACCA‑CCCCCCAAACTTTCGCCAACACAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTaga                                                <  2:431160/213‑1 (MQ=255)
                                                                                                                                                                              aggctCGGGTAAGGGCAATTGC‑AATGCGGGCTGGGCTACTGACCCCATCACCA‑TCGCCCAGATGTTCAACTGCAAAAAATGCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTaga                                                <  1:699217/222‑1 (MQ=255)
                                                                                                                                                                                    gggTAATGGCAGTTCC‑AATGCGGGGGGTGCAACTGACCCATTCACCA‑CCGCCCAGGTTTTCGCAAGCAAAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTAGAGAGTCCAg                                        <  1:119939/228‑1 (MQ=255)
                                                                                                                                                                                         ctggcctgtGC‑AATGCCGGGCGTGCATCTGCACCCCTCACCC‑TCGCCCAGCCTTCCGCCAGCACAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTAGAGAGTCCAGTGCCGc                                  <  1:721944/221‑1 (MQ=255)
                                                                                                                                                                                                           ggCGGAGCTACTGACCCCCTCACCA‑TCGCGCAGACTTTCGCCAGCACAAAATTCCCGCCGGTGGTAATGAACTCTTTGCCGAGGTCAAT‑AAAATAGCTAACCCCCTGATGATCCA‑CCGCCCACCACGTGCAGTCATTCAAAACAGCAGGGAAAACATGCATTGCTGAAACGAAAACTTTCTTTAAATGTTGTGGAAGAGAGTCACGTCACGCTCCCCACGCTTTAGcca                 >  2:177461/1‑228 (MQ=255)
                                                                                                                                                                                                            gCGGTGCTACCGACGCCATCAACA‑TCGCCCAGACTTTCGCCAGCACAAAATTCCCGCCGGGGGTGATGACCTCCTCGCCCAGATCAAT‑AAAATAGATAACCCCTTGATTATCCA‑GCCCCCACCACGGGCAAGCAGTCAAATGAGCGGGGGAAACATGCATTGCTGAAACGATTAATTTCTTTAACTGTTTGCGGAAAGAGGCCAGTGCCGCTACCCACGCTTTAGccct                >  2:222965/1‑227 (MQ=255)
                                                                                                                                                                                                                          gCCATCACCA‑TCGCCCAGACTTTCGCCAGCACAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGAAGAGAGTCCAGTGCCGCAACCCACCCTTTAACCGTCGGACGCCCGGTTg  >  2:289036/1‑229 (MQ=255)
                                                                                                                                                                                                                          |                                                                                                                                                                                                                                       
GTCAGACTGCCAATAATCCAGATAGCCGCCAGCACAGGAACCAAAATAATATAACGCGGTTCTGCCTGAAGGCCGCAAAGCAGCAGCGATAATGCTGACAGTGCGATCTCAA‑GCAGAATGATGTATTCGCGCCGTAACAGGCCTAAAGGAAGCGGCCTGCCAGTCGGTTGGAAATGATCGGGTAATGGCAGTTGC‑AATGCTGGCGGTGCTACTGACGCCATCACCA‑TCGCCCAGACTTTCGCCAGCACAAAATTCCCGCCGGTGGTAATGACCTCTTCGCCGAGATCAAT‑AAAATAGATAACACCTTGATTATCCA‑GCGCACACCACGGGCAGTCAGTCAAATGAGCGGGGTAAACATGCATTGCTGAAACGATACATTTCTTTAACTGTTGGCGTAGAGAGTCCAGTGCCGCTACCCACGCTTTAGCCGTCGGACGCCCGGTTG  >  NC_000913/2149685‑2150129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A