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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 371,542 C→T Q102* (CAA→TAA)  mhpC → 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913371,5420CT92.6% 77.9 / ‑0.0 27coding (304/867 nt)mhpC2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (14/11);  minor base . (1/1);  total (15/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.18e-01

CCGCTGGTAGAGGCGGGCTATCGGGTGATCCTGCTGGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATCAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCGGCAAACTGGTGCTGATGGGCGGCGGTACGGGCGGCATGAG  >  NC_000913/371416‑371672
                                                                                                                              |                                                                                                                                  
ccGCTGGTAGAGGCGGGCTATCGGGTGATCCTGCTGGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCg                                                                                                                        <  1:1005697/139‑1 (MQ=255)
     ggTAGAGGCGGGCTATCGGGTGATCCTGCTGGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCaaa                                                                                                                   >  1:1207895/1‑139 (MQ=255)
                             ccTGCTGGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATg                                                                                           <  1:1301280/139‑1 (MQ=255)
                              ctgctgGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATgg                                                                                          >  1:721369/1‑139 (MQ=255)
                                  tgGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCAc                                                                                                             >  2:842471/1‑116 (MQ=255)
                                  tgGATTGTCCGCGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCAc                                                                                                             <  1:842471/116‑1 (MQ=255)
                                                   ggCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATcc                                                                                                               <  2:962522/97‑1 (MQ=255)
                                                   ggCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATcc                                                                                                               >  1:962522/1‑97 (MQ=255)
                                                                            gTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGt                                            >  2:733377/1‑139 (MQ=255)
                                                                             tGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGAT‑AACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGtt                                                                              >  1:546522/1‑103 (MQ=255)
                                                                             tGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGAT‑AACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGtt                                                                              <  2:546522/103‑1 (MQ=255)
                                                                               gTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCgg                                         <  1:1293273/139‑1 (MQ=255)
                                                                                  cgcgATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGc                                                                                                                       >  1:106532/1‑58 (MQ=255)
                                                                                  cgcgATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGc                                                                                                                       <  2:106532/58‑1 (MQ=255)
                                                                                    cgATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGtt                                                                    >  1:436145/1‑107 (MQ=255)
                                                                                    cgATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGtt                                                                    <  2:436145/107‑1 (MQ=255)
                                                                                                     aCGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATcc                                                                                                               >  1:285417/1‑47 (MQ=255)
                                                                                                     aCGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATcc                                                                                                               <  2:285417/47‑1 (MQ=255)
                                                                                                     aCGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCGGCAAACTGGTGCTGATGggcggc                   >  1:1011255/1‑139 (MQ=255)
                                                                                                     aCGAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCGGCAAACCGGTGCTGATGggcggc                   >  1:618502/1‑139 (MQ=255)
                                                                                                       gAATCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCGGCAAACTGGTGCTGATGGGcggcgg                 >  1:1059438/1‑139 (MQ=255)
                                                                                                        aaTCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGtt                                                                    >  2:1103543/1‑87 (MQ=255)
                                                                                                        aaTCCTGAAAAGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGtt                                                                    <  1:1103543/87‑1 (MQ=255)
                                                                                                                  aGCGTGGTGGATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTGGTTGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGGGCGGGTCGGCAAACTGTTGTTGATGGGCGGCGGTACGGGCGGCa      <  2:630003/139‑1 (MQ=255)
                                                                                                                      tggtggATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCGGCAAACTGGTGCTGATGGGCGGCGGTACGGGCGGCATGAg  >  1:871084/1‑139 (MQ=255)
                                                                                                                         tggATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATa                                                                                 <  2:1301/57‑1 (MQ=255)
                                                                                                                         tggATTAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATa                                                                                 >  1:1301/1‑57 (MQ=255)
                                                                                                                              |                                                                                                                                  
CCGCTGGTAGAGGCGGGCTATCGGGTGATCCTGCTGGATTGTCCGGGTTGGGGCAAGAGCGATTCGGTCGTTAATAGTGGTTCGCGATCGGATCTTAATGCACGAATCCTGAAAAGCGTGGTGGATCAACTGGATATCGCCAAAATCCACCTGCTGGGCAACTCGATGGGGGGCCATAGTTCTGTGGCGTTCACCCTTAAATGGCCGGAGCGCGTCGGCAAACTGGTGCTGATGGGCGGCGGTACGGGCGGCATGAG  >  NC_000913/371416‑371672

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