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 F28 I2 R1 28 4.9 280516 80.6% 226095 64.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 2,513,416 T→C F203S (TTT→TCT)  gltS → glutamate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,513,4160TC88.9% 19.6 / ‑3.2 9F203S (TTT→TCT) gltSglutamate transporter
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (4/4);  total (5/4)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCGCTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGC  >  minE/2513346‑2513475
                                                                      |                                                           
gcgcgcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGtt                                                             >  1:13528/1‑71 (MQ=255)
                    cTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGAc                                         >  1:67524/1‑71 (MQ=255)
                          cacGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGAtg                                               <  1:192763/59‑1 (MQ=255)
                                   cGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATg                                    <  1:82099/61‑1 (MQ=255)
                                      tATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTgg                       >  1:257822/1‑71 (MQ=255)
                                        ttCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACg                                        <  1:103552/52‑1 (MQ=255)
                                        ttCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCAt                                     >  1:240683/1‑55 (MQ=255)
                                         tCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACg                                        <  1:4915/51‑1 (MQ=255)
                                          ccGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGAt                                  >  1:79753/1‑56 (MQ=255)
                                                           cccGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCgcgc  >  1:173507/1‑71 (MQ=255)
                                                                      |                                                           
GCGCGCTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGC  >  minE/2513346‑2513475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A