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
A93 F1 I1 R1 15 55.4 3682408 94.4% 3476193 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC REL606 1,733,297 (CGTATGAA)1→2 coding (333/1413 nt) pykF → pyruvate kinase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 1733288 =5 (0.090)75 (1.360) 54/146 0.0 91.5% coding (324/1413 nt) pykF pyruvate kinase
?REL606 = 1733295 9 (0.160)coding (331/1413 nt) pykF pyruvate kinase

TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/1733363‑1733288
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCT  <  REL606/1733295‑1733222
                                                                                                                                                      
TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTT                                                                            >  2:197480/1‑76
 TCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTC                                                                           >  2:1052753/1‑76
   CATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCAT                                                                         <  2:1576396/76‑1
   CATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCAT                                                                         <  2:1158607/76‑1
   CATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCAT                                                                         <  2:474346/76‑1
    ATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATA                                                                        <  2:469973/76‑1
     TACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATAC                                                                       <  1:719842/76‑1
     TACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATAC                                                                       >  2:1116485/1‑76
     TACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATAC                                                                       <  1:1591968/76‑1
      ACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACG                                                                      >  1:1786521/1‑76
      ACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACG                                                                      >  1:1107845/1‑76
       CCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGT                                                                     <  1:322263/76‑1
            CAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCG                                                                >  2:1687681/1‑76
             AGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGC                                                               <  1:423384/76‑1
              GACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCA                                                              <  2:846351/76‑1
                 CATCGTCAACCATTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACC                                                           <  2:482905/76‑1
                 CATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACC                                                           <  2:884340/76‑1
                   TCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCAT                                                         <  1:1705809/76‑1
                    CGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATT                                                        <  1:1077432/76‑1
                     GTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTT                                                       <  1:792142/76‑1
                      TCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTC                                                      <  1:68021/76‑1
                      TCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTC                                                      >  2:91579/1‑76
                      TCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTC                                                      >  2:563694/1‑76
                       CAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACC                                                                 <  2:1773389/64‑1
                       CAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACC                                                                 >  1:1773389/1‑64
                         ACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCT                                                   >  1:1774692/1‑76
                            AGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTT                                                <  2:375592/76‑1
                            AGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTT                                                <  1:661521/76‑1
                              TACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGC                                              <  1:1689141/76‑1
                                   TGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATA                                         >  1:986442/1‑76
                                    GTTGCCAACAGACAGGTCAGTTGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                        <  2:143052/76‑1
                                    GTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                        <  2:161846/76‑1
                                    GTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                        <  2:1591136/76‑1
                                    GTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                        <  1:685258/76‑1
                                    GTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                        <  1:1142792/76‑1
                                     TTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAAC                                       >  1:1708931/1‑76
                                      TGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACA                                      <  2:1095232/76‑1
                                      TGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACA                                      >  1:490219/1‑76
                                       GCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAG                                     <  1:1827805/76‑1
                                       GCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAG                                     <  2:202669/76‑1
                                       GCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAG                                     >  1:1687487/1‑76
                                         CAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGAT                                   >  2:1329727/1‑76
                                         CAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCG                                            <  1:1788395/67‑1
                                         CAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCG                                            >  2:1788395/1‑67
                                          AACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATT                                  >  1:1501606/1‑76
                                            CAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTA                                >  1:118609/1‑76
                                            CAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTA                                <  1:1210124/76‑1
                                             AGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTAT                               >  1:170280/1‑76
                                             AGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTAT                               <  1:1668235/76‑1
                                              GACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATC                              <  1:1576086/76‑1
                                                 AGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGT                           >  1:750891/1‑76
                                                  GGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTG                          <  2:1697342/76‑1
                                                   GTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGG                         >  1:11092/1‑76
                                                     CAGTAGTGAAACCTTCATACGTTCATACGTTACCGCCACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTG                       >  1:1439916/1‑76
                                                     CAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTG                       >  2:1499909/1‑76
                                                     CAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTG                       >  2:510011/1‑76
                                                       GTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAA                     <  2:547997/76‑1
                                                           TGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTA                 <  1:738221/76‑1
                                                           TGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTA                 >  2:408214/1‑76
                                                            GAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAA                >  2:1117406/1‑76
                                                             AAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAA               >  1:3519/1‑76
                                                             AAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAA               >  1:220135/1‑76
                                                              AACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAG              <  1:1102987/76‑1
                                                              AACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAG              <  2:712111/76‑1
                                                               ACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGG             <  1:1455357/76‑1
                                                               ACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGG             >  1:1420925/1‑76
                                                                 CTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGTCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTC           <  2:1642102/76‑1
                                                                 CTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTC           <  1:627936/76‑1
                                                                  TTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCT          >  1:160861/1‑76
                                                                   TCATCCGTTCATACTTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAAGTCTG         <  2:815840/76‑1
                                                                   TCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTG         <  2:235944/76‑1
                                                                   TCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTG         <  2:1060523/76‑1
                                                                     ATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGAC       <  2:357077/76‑1
                                                                      TACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACC      <  1:1644620/76‑1
                                                                      TACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACC      <  1:1286276/76‑1
                                                                         GTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGC   >  1:771471/1‑76
                                                                          TTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCT  >  2:333900/1‑76
                                                                                                                                                      
TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/1733363‑1733288
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCT  <  REL606/1733295‑1733222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A