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
A18 F7 I1 R1 17 36.9 1277160 95.0% 1213302 141.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 4,110,747 G→C intergenic (+62/+784) cdh → / ← yiiQ CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA4,110,7470GC97.8% 155.1 / ‑5.7 46intergenic (+62/+784)cdh/yiiQCDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base C (20/25);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCA  >  NC_000913_3_pae_tpiA/4110607‑4110890
                                                                                                                                            |                                                                                                                                                
gACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGGCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAAAGTCAAGGAAACTGAGTGCCGGATATGAAATCCGACACCTATGAGACTTTATGCGTCCccgcc                                                                                                                                          >  2:21560/1‑149 (MQ=255)
  cacaAAGAAATATACTGTCTCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCcgccgc                                                                                                                                        <  2:124632/149‑1 (MQ=255)
                 tGACGCTTAACCGTGCTGCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑aa                                                                                                                        <  2:580751/149‑1 (MQ=255)
                   aCGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCTCCCCGCCGCGAGCGGTTTCGCC‑AAtt                                                                                                                      <  2:237634/149‑1 (MQ=255)
                   aCGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTCTCGCC‑AAtt                                                                                                                      >  2:421913/1‑149 (MQ=255)
                          aCCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGAt                                                                                                               <  1:284981/149‑1 (MQ=255)
                            cGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTTTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCt                                                                                                             >  1:292316/1‑149 (MQ=255)
                            cGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCt                                                                                                             >  1:292273/1‑149 (MQ=255)
                                     gCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATg                                                                                                    >  1:571163/1‑149 (MQ=255)
                                      ccGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATgg                                                                                                   <  2:139215/149‑1 (MQ=255)
                                        gAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGCGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGt                                                                                                 >  1:54592/1‑149 (MQ=255)
                                        gAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATc                                                                                                              >  1:105495/1‑136 (MQ=255)
                                        gAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATc                                                                                                              <  2:105495/136‑1 (MQ=255)
                                         aGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTc                                                                                                <  2:547909/149‑1 (MQ=255)
                                             aagtCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAATAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTCAGATATGGGTCtttt                                                                                            <  2:170826/146‑1 (MQ=255)
                                                tctgggtcatgaGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGcc                                                                                         <  2:296356/143‑1 (MQ=255)
                                                     atcatcAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCCGGCTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCAc                                                                                    <  2:268860/149‑1 (MQ=255)
                                                     atcatcAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAAGAAAGTAAGTACCGGATAGGAAATCCGCCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATAGGTCTTTTGCCTTCAc                                                                                    >  2:163826/1‑149 (MQ=255)
                                                              gtgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTGAGGCCGCCCCGCCGCGAGCAGTTGCTCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCt                                                                           >  1:149452/1‑149 (MQ=255)
                                                                   aTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                      <  2:292316/149‑1 (MQ=255)
                                                                   aTTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCa                                                                      <  2:292273/149‑1 (MQ=255)
                                                                    ttttGCTGTAAGGCGAAGAGTTAAGGAGAGTAAGTGCCGCATATAAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGCTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAg                                                                     <  2:329048/149‑1 (MQ=255)
                                                                    ttttGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAg                                                                     <  2:34958/149‑1 (MQ=255)
                                                                    ttttGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAg                                                                     >  1:216758/1‑149 (MQ=255)
                                                                              aGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTccc                                                           <  2:216758/149‑1 (MQ=255)
                                                                                gCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTACCTTCACGGCTGCGCTTGCCAGCAACACTCCCCt                                                         >  1:10760/1‑149 (MQ=255)
                                                                                     gagTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTCTCGCCGTATTCAACCAT‑TCAAGATATGAGTTTTTGGTCTTCACGGCTGCGCTTGCCTGCAACACTCCCCTCGTGc                                                    <  2:458523/149‑1 (MQ=255)
                                                                                        ttAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGa                                                 >  1:608099/1‑149 (MQ=255)
                                                                                          aaGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGt                                               <  2:524644/149‑1 (MQ=255)
                                                                                            ggAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGatat                                                                                                     <  2:184557/93‑1 (MQ=255)
                                                                                            ggAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGatat                                                                                                     >  1:184557/1‑93 (MQ=255)
                                                                                               aagtaagtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATCGGTTTCTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAg                                          <  1:21528/149‑1 (MQ=255)
                                                                                                      tGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAaca                                                                >  1:574848/1‑120 (MQ=255)
                                                                                                      tGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAaca                                                                <  2:574848/120‑1 (MQ=255)
                                                                                                       gCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCtt                                  >  2:27667/1‑149 (MQ=255)
                                                                                                         cGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAgc                                         >  2:624655/1‑140 (MQ=255)
                                                                                                         cGGATATGAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAgc                                         <  1:624655/140‑1 (MQ=255)
                                                                                                                gAAATCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTAGTGCCGAGTTTAAGCGCGGCTTCAACGTCct                         >  1:483762/1‑149 (MQ=255)
                                                                                                                    tCCGGCACCTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTcc                     >  1:49833/1‑149 (MQ=255)
                                                                                                                            cTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCtctc               <  2:499617/147‑1 (MQ=255)
                                                                                                                            cTGTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCtctc               >  1:499617/1‑147 (MQ=255)
                                                                                                                              gTCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATa           <  2:571163/149‑1 (MQ=255)
                                                                                                                               tCAGACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATAc          <  1:27667/149‑1 (MQ=255)
                                                                                                                                  gACTTAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCg       >  1:497778/1‑149 (MQ=255)
                                                                                                                                     ttAAGGCCGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGccc    >  1:160583/1‑149 (MQ=255)
                                                                                                                                       aaGGCCGCCCCCCCGGCAGCCGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTCCCTTCACGGCTGCGCCTGGCACAAACACCCCCCTCGTGCGTCGTTGAGCCGCGGCTTCAACGTCCTCTCCTCTCTCAATACCCGCCCCa  <  2:458558/149‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                                
GACACAACGAAATCTACTGACGCTTAACCGTGCTTCAGCCGAGGAAATTCAGGATCATCAGTGTGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGGCGGCCCCGCCGCGAGCGGTTTCGCC‑AATTCTAAGATCTTAAGATATGGGTCTTTTGCCTTCACGGCTGCGCTTGCCAGCAACACTCCCCTCGTGCCGAGTTTAAGCGCGGCTTCAACGTCCTCTCCGCTCTCAATACCCGCCCCA  >  NC_000913_3_pae_tpiA/4110607‑4110890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A