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
A14 F68 I0 R1 683 78.3 2772122 98.0% 2716679 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,090,124 C→G 50.0% intergenic (+78/‑68) hisL → / → hisG his operon leader peptide/ATP phosphoribosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,090,1240CG50.0% ‑4.9 / 20.4 14intergenic (+78/‑68)hisL/hisGhis operon leader peptide/ATP phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base C (4/3);  new base G (3/4);  total (7/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.76e-01

AGAGACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGACTCACGCGAATTGCTGGCG  >  NC_000913/2089986‑2090269
                                                                                                                                           |                                                                                                                                                 
agagACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg                                                                                                                                         <  2:616967/149‑1 (MQ=255)
agagACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGACCACCTTCCgtg                                                                                                                                         <  1:548686/149‑3 (MQ=255)
 gagaCTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGCAATAAAAAAGCCCCCGGAAGGTGATCTTCCggg                                                                                                                                         <  3:631555/149‑1 (MQ=38)
 gagaCTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCgggg                                                                                                                                        <  3:127662/149‑1 (MQ=255)
               acGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg                                                                                                                                         <  3:671836/134‑1 (MQ=255)
               acGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGGTGATCTTCCggg                                                                                                                                         >  4:671836/1‑134 (MQ=255)
                                        catcaccatcatcCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGtt                                                                                                 >  2:584377/1‑149 (MQ=255)
                                            accatcatcCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTaaa                                                                                             <  1:584377/149‑1 (MQ=255)
                                                                                        aTTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTc                                                                                                          <  1:412064/92‑1 (MQ=255)
                                                                                        aTTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTc                                                                                                          >  2:412064/1‑92 (MQ=255)
                                                                                                                                 cccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGACTCACGCGAAtt         >  3:42405/1‑149 (MQ=255)
                                                                                                                                 cccGGAAGGTGATCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGACTCACGCGAAtt         >  4:162307/1‑149 (MQ=255)
                                                                                                                                  ccGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGACTCACGCGAATTg        >  1:327127/1‑149 (MQ=255)
                                                                                                                                        gATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGACTCACGCGAATTGCTGgcg  >  2:473879/1‑149 (MQ=255)
                                                                                                                                           |                                                                                                                                                 
AGAGACTTTTATGACACGCGTTCAATTTAAACACCACCATCATCACCATCATCCTGACTAGTCTTTCAGGCGATGTGTGCTGGAAGACATTCAGATCTTCCAGTGGTGCATGAACGC‑ATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCGGTTGATAACGGTTCAGACAGGTTTAAAGAGGAATAACAAAATGACAGACAACACTCGTTTACGCATAGCTATGCAGAAATCCGGCCGTTTAAGTGATGACTCACGCGAATTGCTGGCG  >  NC_000913/2089986‑2090269

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A