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 F31 I0 R1 60 36.5 1781264 89.9% 1601356 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,196,245 T→C 100% L375M (TTA→CTG)  icd → isocitrate dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,196,2450TC100.0% 26.6 / NA 14L375M (TTA→CTG) icdisocitrate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/4);  total (10/4)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGA  >  NC_000913/1196115‑1196315
                                                                                                                                  |                                                                      
aTGTGCCCTGTTTGAAGTCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg                                                            <  1:611838/143‑1 (MQ=37)
             gAAGCAACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGTTGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGgcgc                                               >  2:736359/1‑143 (MQ=25)
                gCCACCCATGGTACTGCGCCGAAATAGGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAAt                                            <  2:228379/143‑1 (MQ=25)
                     ccacGGTACTGCGCCGAACTATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGGAATGATGCTGCGCCATATGGGATGGCCTGAAGCGGCTGACCGGGATGTCAAAGATATGGAAGGCGCAACCaatg                                       >  2:174422/1‑141 (MQ=255)
                     ccacGGTACTGCGCCGAAATATGGCTGTCAGGACAAAGTAACTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGTGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatg                                       <  2:593965/143‑3 (MQ=21)
                        cGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTCGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatgcca                                    <  1:17134/143‑6 (MQ=21)
                           tACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaaga                                 >  1:888039/1‑141 (MQ=21)
                                    gAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGCCCTGATTGTCAAAGGCATGGAAGGCGCAATCAATGTCAAGACAGTAActt                        >  1:157820/1‑141 (MQ=18)
                                         atGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGAc                   >  1:270534/1‑143 (MQ=17)
                                         atGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTAGTTTCTCCGCATAGATGATGCTGCGCCATATGGGTCGCACTGAAACGGCTGACCTGATTGGTAAAGGTATGGAAGGCGGCATCAATGACAAGAACGTAACTTAtcga                   >  2:394045/1‑140 (MQ=255)
                                            ccGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGACGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCGATCAATGCCAAGACCGTCACTTATGACttg                >  2:567852/1‑142 (MQ=17)
                                             cGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGAGTTCg               >  1:317602/1‑143 (MQ=17)
                                                         aGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACTGAATCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCTATGCCAAGAGCGTCACTTATGGCGTGGAACGTATcatgg   >  2:798963/1‑143 (MQ=14)
                                                          gTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatgga  >  2:436177/1‑143 (MQ=11)
                                                                                                                                  |                                                                      
ATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGA  >  NC_000913/1196115‑1196315

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A