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
A2 F1 I1 R1 404 265.1 10478538 96.8% 10143224 150.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009974 1,897,927 A→G intergenic (‑5705/‑2892) RPPX_08470 ← / → RPPX_08480 tryptophan synthase subunit beta/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0099741,897,9270AG94.7% 17.8 / ‑4.7 19intergenic (‑5705/‑2892)RPPX_08470/RPPX_08480tryptophan synthase subunit beta/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (6/12);  total (7/12)
Fisher's exact test for biased strand distribution p-value = 3.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GGGCGATGACGTCTACCAGGACGCAGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATATAGACGGTCACACCTTTGAGAACCTGGAACTGGGTGGTGCTGCTTCGGTTCAAGTGACCGACACCACCGACGAAGTAGTGGCCAAGCTGACCGCGACCCCGTCGGTCACCGAAGGGGTGG  >  CP009974/1897789‑1897970
                                                                                                                                          |                                           
aggCGATGACGTCTACAACGATGCTGGCCAGATCAGCCTGGGAATCAATTCGGCGGTAGACGCCACCGGCGCAACGTTCGCGAACCTGCAGTTGGGCGGTGCGGCTACTGCTCAAGTCACCGACACCACCGACGAAGTAGTGGCCaaccgg                                 >  2:3850860/2‑147 (MQ=255)
          gTCTACCAGGACGCTGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGAccc                       >  2:4599376/1‑151 (MQ=1)
          gTCTACCAGGACGCTGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGAccc                       >  1:4348110/1‑151 (MQ=11)
               ccAGGAGGCTGGCCAGATCAGTCTGGGTTTCTCGTCCGGTGTCGGCGTCGACGGTCACACCCTCGCGAACCTTGCACTGGGCGCTGCTGCTCCGGGCCAGGCGACCAACACCCTCGCCGAAGTGTTGGCCAAGCTGACCGCGACCCCTTCg                  <  2:3387889/151‑1 (MQ=9)
                      gctggCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCg           >  2:2468115/4‑151 (MQ=1)
                        tggCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGaa         <  1:377474/150‑1 (MQ=11)
                         ggCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAg        <  2:3927595/151‑1 (MQ=11)
                          gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       <  2:1620187/151‑1 (MQ=11)
                          gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       >  1:832766/1‑151 (MQ=11)
                          gCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAgg       <  1:4941884/151‑1 (MQ=11)
                           ccAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggc      <  1:655805/151‑2 (MQ=11)
                           ccAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggc      <  1:3369970/151‑2 (MQ=11)
                           ccAGATCAGTCTGGGCATCACGTCCGCAGTGGATGTAGGCGGTCACACCTTGAACTAGCTGGAACCGGGCGGAGCTGCTACGGATCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCATCGGACAccacaggc      >  2:2733626/1‑145 (MQ=2)
                            cAGATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcg     <  2:1309881/151‑3 (MQ=11)
                              gATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggt   <  2:3309825/151‑5 (MQ=11)
                              gATCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggt   <  1:4683847/151‑5 (MQ=11)
                               aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  <  1:1790126/151‑6 (MQ=11)
                               aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  <  2:3244116/151‑6 (MQ=11)
                               aTCAGTCTGGGCATCACGTCCGCTGTGGATGTAGACGGTCACACCTTCGAGAACCTGGAACTGGGCGGTGCTGCTTCGGTTCAAGTGACCGACACCCTCGACGAAGTGGTGGCCAAGCTGACCGCGACCCCTTCGGTCACCGAAggcggtg  >  2:4473820/1‑146 (MQ=11)
                                                                                                                                          |                                           
GGGCGATGACGTCTACCAGGACGCAGGCCAGATCAGTCTGGGCATCACGTCCGCTGTGGATATAGACGGTCACACCTTTGAGAACCTGGAACTGGGTGGTGCTGCTTCGGTTCAAGTGACCGACACCACCGACGAAGTAGTGGCCAAGCTGACCGCGACCCCGTCGGTCACCGAAGGGGTGG  >  CP009974/1897789‑1897970

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A