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
A0 F0 I1 R1 336 367.5 14491858 96.8% 14028118 150.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009974 768,193 A→G G462G (GGT→GGC)  RPPX_03350 ← acetolactate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP009974768,1930AG94.4% 24.7 / ‑3.8 18G462G (GGT→GGC) RPPX_03350acetolactate synthase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (13/4);  total (13/5)
Fisher's exact test for biased strand distribution p-value = 2.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

GCCGTTTGCGCCGTAGGCTTCGGCATACTTGACGAAGTCCGGGTTGCCGTAGTCCAGGCCGAAATCGGTGAAGCCCATGTTGGCCTGCTTCCAGCGGATCATGCCGTAACCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGCCGAT  >  CP009974/768085‑768340
                                                                                                            |                                                                                                                                                   
gcggTTTGCGCCGTAGGCTTCGGCATACTTGACGAAGTCCGGGTTGCCGTAGTCCAGGCCGAAATCGGTGAAGCCCATGTTGGCCTGCTTCCAGCGGATCATGCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGa                                                                                                           <  2:3489073/148‑1 (MQ=1)
                                                   gtgcAGGCCGAAATCGGTGAAGCCCATGTTGGCCTGCTTCCAGCGGATCATGCCGTAACCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCca                                                        <  2:6174610/148‑1 (MQ=1)
                                                                                                   cATGCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCAtt        >  1:3486423/1‑151 (MQ=11)
                                                                                                   cATGCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCAtt        >  2:2535483/1‑151 (MQ=11)
                                                                                                     tGCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGc      >  1:896354/1‑151 (MQ=14)
                                                                                                      gacGTAGCGGTCGAGACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTAGTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCTTCGCCACACACCGGGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     <  2:1222936/149‑1 (MQ=11)
                                                                                                      gCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     >  2:2676876/1‑151 (MQ=14)
                                                                                                      gCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     >  2:2677445/1‑151 (MQ=14)
                                                                                                      gCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     >  1:2990831/1‑151 (MQ=17)
                                                                                                      gCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     >  2:2671208/1‑151 (MQ=14)
                                                                                                      gCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     >  1:3639912/1‑151 (MQ=14)
                                                                                                      gCCGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGcc     >  1:3639876/1‑151 (MQ=14)
                                                                                                      gCCGTAGCCGTCGTCACGCAGCATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCGGCCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGCTTGCCGGGCGGTCCGGGCCCCCCAGGGCCGCCGCCATTGcc     >  2:4424301/1‑151 (MQ=11)
                                                                                                       ccGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGCCg    >  1:5082719/1‑151 (MQ=14)
                                                                                                        cGTAGCTGTCGGCACGCAGGATCACCACGGTGATGTGCATGCCCGGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCAGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGCCGa   <  2:6267371/151‑1 (MQ=255)
                                                                                                        cGTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACCCACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGCCGa   >  2:3095112/1‑151 (MQ=14)
                                                                                                         gTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGCCGAt  <  2:6687904/151‑1 (MQ=17)
                                                                                                         gTAGCCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGACCAGGCATTGCCGAt  >  2:5268683/1‑151 (MQ=9)
                                                                                                            |                                                                                                                                                   
GCCGTTTGCGCCGTAGGCTTCGGCATACTTGACGAAGTCCGGGTTGCCGTAGTCCAGGCCGAAATCGGTGAAGCCCATGTTGGCCTGCTTCCAGCGGATCATGCCGTAACCGTCGTCACGCAGGATCACCACGGTGATGTGCATGCCCAGACGTACTGCAGTTTCCAGTTCCTGGCTGTTCATCATGAAGCCGCCGTCGCCACACACCGAGATTACCGGGCGGTCCGGGTGCACCAGGTGCGCAGCCATTGCCGAT  >  CP009974/768085‑768340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A