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
A9 F1 I1 R1 64 69.7 3300380 93.4% 3082554 111.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,512,258 (T)5→6 coding (449/1239 nt) mntH ← manganese/divalent cation transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,512,2531.T100.0% 197.8 / NA 57P152T (CCG→ACG) mntHmanganese/divalent cation transporter
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (28/29);  total (28/29)

GGTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGG‑TTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGG  >  NC_000913/2512132‑2512380
                                                                                                                          |                                                                                                                               
ggTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGt                                                                                                                 >  1:1539820/1‑139 (MQ=255)
  tAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                               <  2:1539820/139‑1 (MQ=255)
  tAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                               <  1:1499558/139‑1 (MQ=255)
         gggATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCAtt                                                                                                        <  1:479390/139‑1 (MQ=255)
                         tACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTcg                                                                                        >  1:1033619/1‑139 (MQ=255)
                         tACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTcg                                                                                        >  2:875602/1‑139 (MQ=255)
                           cccAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCAtt                                                                                                        <  2:1449780/121‑1 (MQ=255)
                           cccAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCAtt                                                                                                        >  1:1449780/1‑121 (MQ=255)
                              aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTACGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATc                                                                                   >  1:1161549/1‑139 (MQ=255)
                              aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATc                                                                                   <  2:53341/139‑1 (MQ=255)
                              aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATc                                                                                   >  1:1243839/1‑139 (MQ=255)
                              aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATc                                                                                   <  1:658492/139‑1 (MQ=255)
                                cTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTTCAGCATTAAAATCAGGACAGTCGCGATccc                                                                                 >  1:536826/1‑139 (MQ=255)
                                cTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATccc                                                                                 >  2:941343/1‑139 (MQ=255)
                                   cgcCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGt                                                                              >  1:1027105/1‑139 (MQ=255)
                                          ttAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCAcc                                                                       >  1:395232/1‑139 (MQ=255)
                                           tAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACcg                                                                      <  2:1161549/139‑1 (MQ=255)
                                                  ggAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCAtt                                                                                                        >  1:428857/1‑98 (MQ=255)
                                                  ggAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCAtt                                                                                                        <  2:428857/98‑1 (MQ=255)
                                                  ggAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTg                                                               >  2:229684/1‑139 (MQ=255)
                                                  ggAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTg                                                               >  1:490495/1‑139 (MQ=255)
                                                  ggAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTg                                                               >  1:628197/1‑139 (MQ=255)
                                                   gagaAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGc                                                              >  1:1077123/1‑139 (MQ=255)
                                                      aaaaTCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGcaac                                                           <  2:305880/139‑1 (MQ=255)
                                                        aaTCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTaaa                                                                                                     <  1:603296/95‑1 (MQ=255)
                                                        aaTCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTaaa                                                                                                     >  2:603296/1‑95 (MQ=255)
                                                        aaTCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGcaacaa                                                         >  1:484723/1‑139 (MQ=255)
                                                            aaCTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                               <  2:1606922/81‑1 (MQ=255)
                                                            aaCTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                               >  1:1606922/1‑81 (MQ=255)
                                                              cTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAac                                                   >  1:668325/1‑139 (MQ=255)
                                                                cGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGa                                                                                                                    <  2:111940/72‑1 (MQ=255)
                                                                cGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGa                                                                                                                    >  1:111940/1‑72 (MQ=255)
                                                                 gACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACAcc                                                <  2:668325/139‑1 (MQ=255)
                                                                       gTAAGCCGCGGCAACAAACTACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                          <  1:206469/139‑1 (MQ=255)
                                                                       gTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                          <  2:1077123/139‑1 (MQ=255)
                                                                       gTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                          <  2:628197/139‑1 (MQ=255)
                                                                       gTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                          <  1:229684/139‑1 (MQ=255)
                                                                             cgcgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGa                                                      <  2:1509822/121‑1 (MQ=255)
                                                                             cgcgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGa                                                      >  1:1509822/1‑121 (MQ=255)
                                                                                ggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGa                                                                                              >  2:1639976/1‑78 (MQ=255)
                                                                                ggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGa                                                                                              <  1:1639976/78‑1 (MQ=255)
                                                                                ggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaaa                                 >  2:814957/1‑139 (MQ=255)
                                                                                 gCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                               >  1:147803/1‑60 (MQ=255)
                                                                                 gCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                               <  2:147803/60‑1 (MQ=255)
                                                                                         caacaGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgc                        <  1:92620/139‑1 (MQ=255)
                                                                                           acaGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccg                      <  1:1016308/139‑1 (MQ=255)
                                                                                           acaGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccg                      <  2:1231158/139‑1 (MQ=255)
                                                                                             aGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCa                    <  1:607389/139‑1 (MQ=255)
                                                                                                 aCCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCaa                <  1:128617/139‑1 (MQ=255)
                                                                                                    cGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccg                      >  1:748721/1‑130 (MQ=255)
                                                                                                    cGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccg                      <  2:748721/130‑1 (MQ=255)
                                                                                                      ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACg                                                                                                                  <  2:1545588/36‑1 (MQ=255)
                                                                                                      ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACg                                                                                                                  >  1:1545588/1‑36 (MQ=255)
                                                                                                      ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                          <  1:1391304/108‑1 (MQ=255)
                                                                                                      ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                          >  2:1391304/1‑108 (MQ=255)
                                                                                                      ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAAt           >  1:374292/1‑139 (MQ=255)
                                                                                                               ttCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAgg  <  2:395232/139‑1 (MQ=255)
                                                                                                                          |                                                                                                                               
GGTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGG‑TTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCAGG  >  NC_000913/2512132‑2512380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A