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 I1 R1 315 33.5 1889570 98.7% 1865005 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,082,793 G→A intergenic (+122/+84) loiP → / ← speB metalloprotease LoiP/agmatinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,082,7930GA100.0% 178.7 / NA 48intergenic (+122/+84)loiP/speBmetalloprotease LoiP/agmatinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/28);  total (20/28)

TCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATC  >  NC_000913/3082718‑3082865
                                                                           |                                                                        
tCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGcc                                                                     >  1:574704/1‑81 (MQ=255)
    aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGcc                                                                     <  1:574632/77‑1 (MQ=255)
    aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGcc                                                                     <  2:574636/77‑1 (MQ=255)
    aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCg                                                                    <  1:574635/78‑1 (MQ=255)
    aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGaa                                                                  <  2:574634/80‑1 (MQ=255)
    aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGaa                                                                  <  1:574631/80‑1 (MQ=255)
    aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGaa                                                                  <  1:574633/80‑1 (MQ=255)
          aTGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGt                                                           <  1:574637/81‑1 (MQ=255)
             gCACATTTGTTACCTTGTGCGCATTGGCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCgg                                                        <  1:574639/81‑1 (MQ=255)
             gCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCgg                                                        <  2:574638/81‑1 (MQ=255)
             gCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCgg                                                        <  2:574640/81‑1 (MQ=255)
                caTTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATa                                                     <  1:574641/81‑1 (MQ=255)
                 aTTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATaa                                                    <  2:574642/81‑1 (MQ=255)
                    tGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGc                                                 >  1:574739/1‑81 (MQ=255)
                     gTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGc                                                 <  2:574643/80‑1 (MQ=255)
                      ttACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCg                                                <  1:574645/80‑1 (MQ=255)
                      ttACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGt                                               <  1:574644/81‑1 (MQ=255)
                      ttACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGt                                               <  1:574646/81‑1 (MQ=255)
                        aCCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGtt                                              <  2:574647/80‑1 (MQ=255)
                        aCCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGtt                                              >  2:574711/1‑80 (MQ=255)
                          cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           <  2:574649/81‑1 (MQ=255)
                          cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           >  1:574731/1‑81 (MQ=255)
                          cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           <  1:574650/81‑1 (MQ=255)
                          cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           <  1:574648/81‑1 (MQ=255)
                             gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAcgcc                                        >  2:574719/1‑81 (MQ=255)
                                  cATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATc                                   <  1:574651/81‑1 (MQ=255)
                                   aTTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATcc                                  >  2:574740/1‑81 (MQ=255)
                                     tGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGa                                >  1:574720/1‑81 (MQ=255)
                                      gCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGa                                >  1:574718/1‑80 (MQ=255)
                                        cGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAt                             >  2:574730/1‑81 (MQ=255)
                                         ggATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAt                             >  1:574723/1‑80 (MQ=255)
                                          gatgcgatgcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAtt                            >  1:574714/1‑80 (MQ=255)
                                              cgatgcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                       >  1:574717/1‑81 (MQ=255)
                                                  gcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACg                   >  1:574756/1‑81 (MQ=255)
                                                  gcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACg                   >  2:574736/1‑81 (MQ=255)
                                                      gcgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGtttt               <  1:574654/81‑1 (MQ=255)
                                                      gcgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGtttt               <  2:574653/81‑1 (MQ=255)
                                                      gcgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGtt                 <  1:574652/79‑1 (MQ=255)
                                                       cgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTa              <  1:574655/81‑1 (MQ=255)
                                                           tCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCg          >  2:574745/1‑81 (MQ=255)
                                                             ttATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTg        >  2:574724/1‑81 (MQ=255)
                                                              tATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTgc       >  2:574725/1‑81 (MQ=255)
                                                              tATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTgc       >  1:574738/1‑81 (MQ=255)
                                                               aTCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGt         <  1:574657/78‑1 (MQ=255)
                                                               aTCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTg        <  1:574656/79‑1 (MQ=255)
                                                                  cGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcat   >  2:574722/1‑81 (MQ=255)
                                                                   ggCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatc  <  1:574658/81‑1 (MQ=255)
                                                                   ggCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatc  >  1:574766/1‑81 (MQ=255)
                                                                           |                                                                        
TCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATC  >  NC_000913/3082718‑3082865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A