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
A26 F1 I1 R1 14 45.0 2861610 96.8% 2770038 76.0

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 =12 (0.270)52 (1.190) 35/146 0.3 86.9% coding (324/1413 nt) pykF pyruvate kinase
?REL606 = 1733295 4 (0.090)coding (331/1413 nt) pykF pyruvate kinase

TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/1733363‑1733288
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCTT  <  REL606/1733295‑1733221
                                                                                                                                                       
TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACCGGTCAGTAGTGAAACCTTCATACGTT                                                                             >  1:811524/1‑76
TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTT                                                                             >  1:1318982/1‑76
  CCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCA                                                                           >  2:438689/1‑76
     TACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATAC                                                                        <  1:407475/76‑1
     TACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATAC                                                                        <  2:385076/76‑1
      ACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACG                                                                       <  1:1110653/76‑1
        CGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGAGAGGTCAGTAGTGAAACCTTCATACGTTCATACGTT                                                                     <  1:339511/76‑1
        CGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTT                                                                     <  1:339498/76‑1
         GATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGNTCAGTAGTGAAACCTTCATACGTTCATACGTTA                                                                    <  2:1212935/76‑1
         GATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTA                                                                    <  2:749456/76‑1
           TCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACC                                                                  >  1:669311/1‑76
               ACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCANACGTTACCGCAA                                                              <  1:15771/76‑1
                CCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAAC                                                             <  1:297273/76‑1
                CCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAAC                                                             <  2:750852/76‑1
                    CGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATT                                                         >  1:387356/1‑76
                    CGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATT                                                         >  1:1189865/1‑76
                       CAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCG                                                      >  1:1400004/1‑76
                         ACCAGTTCGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCACACGTTCATACGTTACCGCAACCATTTCGCT                                                    <  1:1307705/76‑1
                         ACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCT                                                    <  1:438689/76‑1
                          CCAGTACGGTGTTGCCAACATANNGGTCAGTAGTNNCACCTTCACACGTTTATACGTTACCGCAACCATTTCGCTG                                                   <  1:1286282/76‑1
                           CAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGT                                                  <  2:490126/76‑1
                            AGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTT                                                 <  1:244757/76‑1
                            AGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTT                                                 <  2:62967/76‑1
                            AGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTT                                                 <  2:62984/76‑1
                              TACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGC                                               >  2:229629/1‑76
                              TACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGC                                               >  1:805016/1‑76
                               ACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTGACCGCAACCTTTTCGCTGTTGCC                                              >  1:1218515/1‑76
                                  GTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGAT                                           <  2:817724/76‑1
                                  GTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGAT                                           <  2:375487/76‑1
                                   TGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCCTTTCGCTGTTGCCGctc                                          >  1:430593/1‑73
                                   TGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATA                                          >  1:430570/1‑76
                                   TGTTGCCAACAGACAGGTCAGTAGTAAAACCCTCATACGANNATACGTTACCNNATCCATTTCGCTGTTGCCGATA                                          >  1:1284119/1‑76
                                    GTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                         <  2:894379/76‑1
                                    GTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAA                                         <  1:1236789/76‑1
                                     TTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAAC                                        <  1:1320328/76‑1
                                     TTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAAC                                        <  1:630570/76‑1
                                          AACAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATT                                   <  2:921420/76‑1
                                            CAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTA                                 >  1:241196/1‑76
                                            CAGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTA                                 >  1:368298/1‑76
                                             AGACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTAT                                >  1:969997/1‑76
                                             AGACAGGTCAGTAGNGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTAn                                <  2:208280/76‑2
                                               ACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCA                              >  2:683145/1‑76
                                               ACAGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGACTCATCA                              >  2:1358501/1‑76
                                                 AGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGT                            >  1:463639/1‑76
                                                 AGGTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGT                            <  1:1106294/76‑1
                                                   GTCAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGAATTATCAGTGG                          <  1:1320441/76‑1
                                                     CAGTAGTGAAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTG                        <  2:1424715/76‑1
                                                             AAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAA                >  2:640073/1‑76
                                                             AAACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAA                <  2:642033/76‑1
                                                              acCCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAG               <  2:535656/74‑1
                                                              AACCTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAG               >  2:1376506/1‑76
                                                                 CTTCATACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTC            >  2:1126596/1‑76
                                                                       ACGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCTGTGGTGAAAGTAAAGGTCTGACCA      <  2:811524/76‑1
                                                                        CGTTCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAG     <  1:279734/76‑1
                                                                           TCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCTT  <  2:676315/76‑1
                                                                           TCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCTT  <  2:20825/76‑1
                                                                           TCATACGTTACCGCAACCATTTCGCTGGTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCTg  <  2:676301/76‑2
                                                                                                                                                       
TTCCATACCGATCAGACCATCGTCAACCAGTACGGTGTTGCCAACAGACAGGTCAGTAGTGAAACCTTCATACGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/1733363‑1733288
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttCATACGTTACCGCAACCATTTCGCTGTTGCCGATAACAGATTTATCAGTGGTGAAAGTAAAGGTCTGACCAGCTT  <  REL606/1733295‑1733221

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