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
A4 F73 I1 R1 27 19.6 661800 98.9% 654520 139.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,515,609 C→A intergenic (+166/+34) insL‑3 → / ← pdeA putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,515,6090CA100.0% 17.1 / NA 7intergenic (+166/+34)insL‑3/pdeAputative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (3/4);  total (3/4)

CAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCG  >  NC_000913/2515484‑2515700
                                                                                                                             |                                                                                           
cacgTGGCCATTCGTGCCTCAGTATCCCGAACAGCCTCCAAAACGTAAATGAAGATCCCGAGGCATACGCCTAACGAGGCACCGAGGCGTCGCATTCTTCAGTTGGTTCAACCCTTAAGCTAGCGATTAGGGGATAATTc                                                                               >  2:216071/4‑140 (MQ=2)
cAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTCCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTc                                                                               >  1:303622/1‑140 (MQ=18)
             gTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTa                                                                  <  2:203626/140‑1 (MQ=255)
                        tCCCTGACAGCCTACAAAACGCAATTGAAGACCGCGAGGCATCGCCTTACCGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAAt                                                       <  2:285580/140‑1 (MQ=255)
                                             cAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGAc                                  <  1:121830/140‑1 (MQ=255)
                                                ttGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCaa                               <  1:25228/140‑1 (MQ=255)
                                                          cgAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATAccc                     >  1:60706/1‑140 (MQ=255)
                                                          cgAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATAccc                     >  2:141193/1‑140 (MQ=255)
                                                                             ggCACCGTGGCGCCGCATTCTTCAGATGGCTCAACCCTTAAGTTAGCGATTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCg  >  2:249384/1‑140 (MQ=255)
                                                                                                                             |                                                                                           
CAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGATAATTCCCCGGTTTTTTTACGCCTGTTAATCAGCTAATGGCTGCGGGCGACCAATCAAATACCCTTGCAGATATTGCACCCCG  >  NC_000913/2515484‑2515700

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A