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 F5 I177 R1 141 27.5 996908 97.7% 973979 124.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,041,277 T→C intergenic (‑18/+28) gfcE ← / ← gfcD polysaccharide export protein/YjbH domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,041,2770TC100.0% 13.3 / NA 5intergenic (‑18/+28)gfcE/gfcDpolysaccharide export protein/YjbH domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (2/3);  total (2/3)

AGGTAGTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCT  >  NZ_CP009273/1041140‑1041330
                                                                                                                                         |                                                     
aGGTAGTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGt                                                       <  2:151885/138‑1 (MQ=255)
aGGTAGTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGt                                                       <  2:206399/138‑1 (MQ=255)
     gTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCaatg                                                  <  2:226128/138‑1 (MQ=255)
        cAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCaatgta                                                <  1:36561/137‑1 (MQ=255)
        cAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCaatgta                                                >  2:36561/1‑137 (MQ=255)
                            gTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGt                                                       >  1:229197/1‑110 (MQ=255)
                            gTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGt                                                       <  2:229197/110‑1 (MQ=255)
                            gTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGt                           >  2:346503/1‑138 (MQ=255)
                             tCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTa                         <  2:85111/139‑1 (MQ=255)
                                                                                                                                         tCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGct  >  1:193238/1‑54 (MQ=255)
                                                                                                                                         tCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGct  <  2:193238/54‑1 (MQ=255)
                                                                                                                                         |                                                     
AGGTAGTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCT  >  NZ_CP009273/1041140‑1041330

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A