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
A1 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,773,602 T→C V441A (GTT→GCT)  mtlA → mannitol‑specific PTS enzyme: IIA, IIB and IIC components

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,773,6020TC100.0% 76.2 / NA 22V441A (GTT→GCT) mtlAmannitol‑specific PTS enzyme: IIA, IIB and IIC components
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/9);  total (13/9)

TTCAGGATGCAGGTCTGTCGCAGATTTCTGTTACTAACAGCGCGATCAACAACCTGCCGCCAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGTTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAGAGAAAGTAAAAGACAGCC  >  NC_000913/3773485‑3773724
                                                                                                                     |                                                                                                                          
ttCAGGATGCAGGTCTGTCGCAGATTTCTGTTACTAACAGCGCGATCAACAACCTGCCGCCAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTc                                                                                                       >  2:700785/1‑139 (MQ=255)
                                      aGCGCGAGCAACAACCTGCCGCCAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGATCGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGcc                                                                 >  2:742890/1‑139 (MQ=255)
                                           gATCAACAACCTGCCGCCAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGAcc                                                            <  2:346749/139‑1 (MQ=255)
                                                       gccgccAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGtt                                                >  2:1030284/1‑139 (MQ=255)
                                                        ccgccAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTg                                                                           <  1:22590/111‑1 (MQ=255)
                                                        ccgccAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTg                                                                           >  2:22590/1‑111 (MQ=255)
                                                                         cGTCATCACTCACCGTGACCTGACCCAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAACGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACg                              >  2:929756/1‑139 (MQ=255)
                                                                          gTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCacac                               <  1:189052/137‑1 (MQ=255)
                                                                          gTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCacac                               >  2:189052/1‑137 (MQ=255)
                                                                                actcacCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGGCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACg                       <  1:11618/139‑1 (MQ=255)
                                                                                    acCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAaga                   >  1:188641/1‑139 (MQ=255)
                                                                                    acCGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAaga                   <  1:742890/139‑1 (MQ=255)
                                                                                      cGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAgaga                 <  2:188641/139‑1 (MQ=255)
                                                                                      cGTGACCTGACCGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAgaga                 >  1:558079/1‑139 (MQ=255)
                                                                                          acctgaccGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAGAGAAAGt             >  2:101659/1‑139 (MQ=255)
                                                                                               accGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAGAGAAAGTAAAAg        >  1:221836/1‑139 (MQ=255)
                                                                                                ccGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCacac                               <  1:801594/115‑1 (MQ=255)
                                                                                                ccGAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCacac                               >  2:801594/1‑115 (MQ=255)
                                                                                                  gAACGCGCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAGAGAAAGTAAAAGACa     <  2:558079/139‑1 (MQ=255)
                                                                                                     cgcgCTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAGAGAAAGTAAAAGACAGcc  >  2:620517/1‑139 (MQ=255)
                                                                                                         cTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACa                                                                                   <  2:45838/54‑1 (MQ=255)
                                                                                                         cTATGCGCCAGGCTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACa                                                                                   >  1:45838/1‑54 (MQ=255)
                                                                                                                     |                                                                                                                          
TTCAGGATGCAGGTCTGTCGCAGATTTCTGTTACTAACAGCGCGATCAACAACCTGCCGCCAGATGTGGACCTCGTCATCACTCACCGTGACCTGACCGAACGCGCTATGCGCCAGGTTCCGCAGGCACAGCATATTTCGCTGACCAACTTCCTCGACAGCGGCCTGTACACCAGCCTGACCGAACGTCTGGTTGCTGCCCAACGCCACACGGCAAACGAAGAGAAAGTAAAAGACAGCC  >  NC_000913/3773485‑3773724

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A