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
A9 F17 I0 R1 82 23.7 530958 91.4% 485295 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,187,071 C→T 100% R331K (AGA→AAA)  rsbU ← sigma factor B regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,187,0710CT100.0% 59.9 / NA 18R331K (AGA→AAA) rsbUsigma factor B regulator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (7/11);  total (7/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch.

ATTCATTTCATTACACTCCTACTTATTAAAAATATTTATCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTCTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCATATGTTTATGTTTTTTAATATATTCTAAAAGTTTTTGTTT  >  CP000730/2186937‑2187207
                                                                                                                                      |                                                                                                                                        
aTTCATTTCATTACACTCCTACTTATTAAAAATATTTATCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTta                                                                                                                                    <  2:260096/141‑1 (MQ=255)
                tCCTACTTATTAAAAATATTTATCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCat                                                                                                                    <  2:11310/141‑1 (MQ=255)
                tCCTACTTATTAAAAATATTTATCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCat                                                                                                                    <  2:176005/141‑1 (MQ=255)
                                     aTCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGtt                                                                                               <  1:200226/141‑1 (MQ=255)
                                     aTCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGtt                                                                                               <  1:262319/141‑1 (MQ=255)
                                           aTTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAg                                                                                         >  1:218321/1‑141 (MQ=255)
                                                 aGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTaa                                                                                   <  2:236207/141‑1 (MQ=255)
                                                  gcgcTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTaaa                                                                                  >  1:63773/1‑141 (MQ=255)
                                                  gcgcTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTaaa                                                                                  >  1:149503/1‑141 (MQ=255)
                                                                                     atataCCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTgg                                               >  1:197723/1‑141 (MQ=255)
                                                                                                   ataatTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATTAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCAtatgtttat                                 >  2:155723/1‑141 (MQ=255)
                                                                                                   ataatTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGTTAATTTGGACAATATCTTGTGGGTTCAtgtgtttat                                 >  2:44090/1‑141 (MQ=255)
                                                                                                   ataatTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCAtatgtttat                                 >  1:94392/1‑141 (MQ=255)
                                                                                                     aatTTCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCAtatgtttatgt                               <  1:16991/141‑1 (MQ=255)
                                                                                                         tCTAATCTTCTTTTTTAAATTAATTTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCATATGTTTATGttttt                           <  1:207613/141‑1 (MQ=255)
                                                                                                                           attaattTACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCATATGTTTATGTTTTTTAATATATTCTAAAAGtt         <  2:218321/141‑1 (MQ=255)
                                                                                                                                  tACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCATATGTTTATGTTTTTTAATATATTCTAAAAGTTTTTGttt  <  2:149503/141‑1 (MQ=255)
                                                                                                                                  tACTTTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCATATGTTTATGTTTTTTAATATATTCTAAAAGTTTTTGttt  <  2:63773/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                        
ATTCATTTCATTACACTCCTACTTATTAAAAATATTTATCTTCATTTTAAGCGCTGTATCCACCATATTTATATTTCAAATTATTATATACCCATCGAAATAATTTCTAATCTTCTTTTTTAAATTAATTTACTCTTTTTATAATCAAAATAGTCATATCATCTTTTTTATTTGGGTTTTGAAGCTTTAAAATTGCTTCATAGATAATTTGAACAATATCTTGTGGGTGCATATGTTTATGTTTTTTAATATATTCTAAAAGTTTTTGTTT  >  CP000730/2186937‑2187207

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A