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
A6 F1 I1 R1 750 51.0 2595496 93.6% 2429384 106.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,240,754 (C)5→6 coding (915/1041 nt) galS ← galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,240,7491.C97.9% 166.3 / ‑3.3 48coding (920/1041 nt)galSgalactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (23/24);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CAGATTGAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑CCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTGAG  >  NC_000913/2240614‑2240868
                                                                                                                                        |                                                                                                                        
caGATTGAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑ccc                                                                                                                       <  1:188044/139‑1 (MQ=255)
     tGAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑ccc‑ccctg                                                                                                                 >  2:1223052/1‑136 (MQ=255)
      gAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑ccc‑ccctgc                                                                                                                >  1:1174516/1‑135 (MQ=255)
             gTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCa                                                                                                          >  1:774023/1‑139 (MQ=255)
             gTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCa                                                                                                          >  1:457531/1‑139 (MQ=255)
                  aTCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCg                                                                                                     <  2:457531/139‑1 (MQ=255)
                      ccTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTgg                                                                                                 >  2:548669/1‑139 (MQ=255)
                       cTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGc                                                                                                <  1:1223052/139‑1 (MQ=255)
                          aTTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTaa                                                                                             >  1:868631/1‑139 (MQ=255)
                               ttgAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCg                                                                                        >  1:609234/1‑139 (MQ=255)
                                     tAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTg                                                                                  <  2:1174516/139‑1 (MQ=255)
                                      aGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTGATATCGCCATTGa                                                                                 <  2:868631/139‑1 (MQ=255)
                                      aGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGa                                                                                 <  1:1272384/139‑1 (MQ=255)
                                       gTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGaa                                                                                >  2:713457/1‑139 (MQ=255)
                                         gATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCg                                                                                                     >  2:1200179/1‑116 (MQ=255)
                                         gATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCg                                                                                                     <  1:1200179/116‑1 (MQ=255)
                                              ccgccgcATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAAttt                                                                                          <  2:1095984/122‑1 (MQ=255)
                                              ccgccgcATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAAttt                                                                                          >  1:1095984/1‑122 (MQ=255)
                                                 ccgcATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGAt                                                                      >  2:392057/1‑139 (MQ=255)
                                                    cATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGa                                                                                 >  2:89362/1‑125 (MQ=255)
                                                    cATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGa                                                                                 <  1:89362/125‑1 (MQ=255)
                                                       tCTGGGGTGTTGCGACAGAATGACGACTCTCTAACGTCGGCATGCAACAATAGCTGGGACGAGGTTCAATATTGCGTGGTG‑CCCTCCTTCAAGGCCACTTCTGTGGCTGATTTCTCCATTGAAGCAATGGGATAACGCa                                                                <  2:585101/139‑1 (MQ=255)
                                                       tCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                <  1:1258767/139‑1 (MQ=255)
                                                            cGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTc                                                           >  2:245705/1‑139 (MQ=255)
                                                             gtgtTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCg                                                          >  2:257795/1‑139 (MQ=255)
                                                                ttGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGcc                                                                                                           <  2:991688/87‑1 (MQ=255)
                                                                ttGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGcc                                                                                                           >  1:991688/1‑87 (MQ=255)
                                                                ttGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTa                                                       >  2:1153855/1‑139 (MQ=255)
                                                                 tGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTc                                                                                                      >  1:593475/1‑91 (MQ=255)
                                                                 tGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTc                                                                                                      <  2:593475/91‑1 (MQ=255)
                                                                 tGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTaa                                                      >  2:1163918/1‑139 (MQ=255)
                                                                    gACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTg                                                   <  1:1163918/139‑1 (MQ=255)
                                                                                    aCTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACgg                                   <  1:1153855/139‑1 (MQ=255)
                                                                                        aCGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGTCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGa                               <  2:774023/139‑1 (MQ=255)
                                                                                                        gTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTc                                             <  1:711520/109‑1 (MQ=255)
                                                                                                        gTGGCTGGCACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTc                                             >  2:711520/1‑109 (MQ=255)
                                                                                                           gctggcACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                >  1:1116436/1‑87 (MQ=255)
                                                                                                           gctggcACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                <  2:1116436/87‑1 (MQ=255)
                                                                                                             tggcACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCga          <  1:257795/139‑1 (MQ=255)
                                                                                                                cACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCg                                >  2:62529/1‑114 (MQ=255)
                                                                                                                cACGAGGATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCg                                <  1:62529/114‑1 (MQ=255)
                                                                                                                     ggATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTgag  <  2:609234/139‑1 (MQ=255)
                                                                                                                     ggATCAATATTGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTgag  <  1:713457/139‑1 (MQ=255)
                                                                                                                               tGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                <  2:612545/67‑1 (MQ=255)
                                                                                                                               tGCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                >  1:612545/1‑67 (MQ=255)
                                                                                                                                gCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCaa                                                                            >  1:46678/1‑54 (MQ=255)
                                                                                                                                gCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCaa                                                                            <  2:46678/54‑1 (MQ=255)
                                                                                                                                gCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAat                        >  2:594172/1‑106 (MQ=255)
                                                                                                                                gCCTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAat                        <  1:594172/106‑1 (MQ=255)
                                                                                                                                 ccTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGc                                 <  1:2826/96‑1 (MQ=255)
                                                                                                                                 ccTGCTGCCCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGc                                 >  2:2826/1‑96 (MQ=255)
                                                                                                                                        |                                                                                                                        
CAGATTGAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑CCC‑CCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTGAG  >  NC_000913/2240614‑2240868

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A