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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,669,340 A→G intergenic (‑152/‑252) yhjA ← / → treF putative cytochrome C peroxidase/cytoplasmic trehalase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,669,3400AG98.5% 220.4 / ‑4.2 66intergenic (‑152/‑252)yhjA/treFputative cytochrome C peroxidase/cytoplasmic trehalase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (34/31);  total (34/32)
Fisher's exact test for biased strand distribution p-value = 4.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

TGCAAACGTCTCTGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGATAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCTGAAAATGAAAAACAACACCAAATC  >  NC_000913/3669243‑3669434
                                                                                                 |                                                                                              
tgcAAACGTCTCTGCGACACAAAACCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTa                                                                                              <  2:885889/100‑1 (MQ=255)
 gcAAACGTCTCTGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAg                                                                                             >  2:194987/1‑100 (MQ=255)
   aaaCGTCTCTGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGcc                                                                                           <  1:153290/100‑1 (MQ=255)
     aCGTCTCTGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCtg                                                                                         <  1:887132/100‑1 (MQ=255)
       gTCTCTGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCtgtg                                                                                       <  1:1206610/100‑1 (MQ=255)
         ctctGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAGTCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGcc                                                                                     <  1:811184/100‑1 (MQ=255)
         ctctGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGcc                                                                                     <  1:424274/100‑1 (MQ=255)
         ctctGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGATAGCCTGTGcc                                                                                     <  1:974305/100‑1 (MQ=255)
           ctGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTa                                                                                   <  1:844390/100‑1 (MQ=255)
           ctGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTa                                                                                   >  2:696039/1‑100 (MQ=255)
            tGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTAt                                                                                  <  2:254806/100‑1 (MQ=255)
            tGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTAt                                                                                  >  2:285660/1‑100 (MQ=255)
             gCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTAtt                                                                                 >  2:1014854/1‑100 (MQ=255)
             gCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCATGTGCCTAtt                                                                                 >  2:1511854/1‑100 (MQ=255)
                   cAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAg                                                                           >  1:1255504/1‑100 (MQ=255)
                   cAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGCAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCTTATTACTCa                                                                            >  2:928175/1‑99 (MQ=255)
                      aGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATc                                                                        >  2:20368/1‑100 (MQ=255)
                        ccATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAg                                                                      >  1:594408/1‑100 (MQ=255)
                          atcatAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGa                                                                    >  2:1117364/1‑100 (MQ=255)
                             atAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATg                                                                 >  2:295612/1‑100 (MQ=255)
                                 aaaaCAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTATGCCTATTACCCAGATCAGGAATGGCat                                                             >  2:503855/1‑100 (MQ=255)
                                  aaaCAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCata                                                            <  1:295612/100‑1 (MQ=255)
                                    aCATGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATc                                                          <  2:510146/100‑1 (MQ=255)
                                     cAGGGAGATACGCTTTTTGATAGGCATCAATCAATTACATGAATATAAACTATCAATAAGGTAGAATGTGCCTATTACTCAGATCAGGAATGGCATATCa                                                         >  2:689768/1‑100 (MQ=255)
                                       gggAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATg                                                       <  2:196491/100‑1 (MQ=255)
                                          agaTACGCTTTTTCATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGAt                                                     <  2:368843/99‑1 (MQ=255)
                                           gaTACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTg                                                   >  2:1182620/1‑100 (MQ=255)
                                           gaTACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGGAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTg                                                   >  2:643002/1‑100 (MQ=255)
                                               cGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTgcggc                                               >  2:1195962/1‑100 (MQ=255)
                                               cGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTgcggc                                               >  1:171043/1‑100 (MQ=255)
                                                gCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTgcggcg                                              <  2:1581647/100‑1 (MQ=255)
                                                 cTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCga                                             <  1:1341447/100‑1 (MQ=255)
                                                  tttttGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCgag                                            <  1:896448/100‑1 (MQ=255)
                                                   ttttGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCgaga                                           <  1:395746/100‑1 (MQ=255)
                                                   ttttGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCgag                                            >  2:579618/1‑99 (MQ=255)
                                                       gATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGAGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAg                                       <  1:664636/100‑1 (MQ=255)
                                                         tAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGa                                     >  2:651995/1‑100 (MQ=255)
                                                         tAGGAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGa                                     >  2:60078/1‑100 (MQ=255)
                                                           ggAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGAtt                                   >  2:627039/1‑100 (MQ=255)
                                                           ggAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGAtt                                   >  1:1036106/1‑100 (MQ=255)
                                                            gAATCAATCAATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTg                                  <  1:1156473/100‑1 (MQ=255)
                                                              atcaatcaATTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGaa                                <  2:1208292/100‑1 (MQ=255)
                                                               tcaatcaaTTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAAt                               <  1:875139/100‑1 (MQ=255)
                                                               tcaatcaaTTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAAt                               >  2:27026/1‑100 (MQ=255)
                                                                caatcaatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATg                              <  1:1439440/100‑1 (MQ=255)
                                                                caatcaatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATg                              >  2:430431/1‑100 (MQ=255)
                                                                 aatcaatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGt                             >  2:564331/1‑100 (MQ=255)
                                                                    caatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCt                          >  2:286074/1‑100 (MQ=255)
                                                                    caatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCt                          >  2:480721/1‑100 (MQ=255)
                                                                    caatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCt                          <  1:574124/100‑1 (MQ=255)
                                                                     aatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtg                         >  2:456995/1‑100 (MQ=255)
                                                                     aatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtg                         <  1:164713/100‑1 (MQ=255)
                                                                     aatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtg                         <  2:1149781/100‑1 (MQ=255)
                                                                     aatTACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACAAAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCt                          <  2:43981/99‑1 (MQ=255)
                                                                        tACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTTTTACCCAGATCAGGAATGGGATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaa                      <  2:860321/100‑1 (MQ=255)
                                                                        tACATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaa                      <  1:390467/100‑1 (MQ=255)
                                                                         aCATGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaaa                     <  1:1421321/100‑1 (MQ=255)
                                                                          cATGAATATAAACTATCAATAAGGTAGCCTGTGACTATGACCCAGCTGAAGAATGGGATATCATGATTGTGGCGAGAGCAGCATTGAATGTTCggaacat                    >  2:971337/1‑100 (MQ=255)
                                                                            tGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaaatga                  >  2:652583/1‑100 (MQ=255)
                                                                            tGAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaaatga                  >  1:781465/1‑100 (MQ=255)
                                                                             gAATATAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaaatgaa                 >  1:1148160/1‑100 (MQ=255)
                                                                               atatAAACTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCtgaaaatgaaaa               <  2:1219917/100‑1 (MQ=255)
                                                                                    aaCTATCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCTGAAAATGAAAaacaac          <  2:606600/100‑1 (MQ=255)
                                                                                        aTCAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCTGAAAATGAAAAACAACACCa      >  1:484082/1‑100 (MQ=255)
                                                                                          cAATAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCTGAAAATGAAAAACAACACCaaa    >  1:695172/1‑100 (MQ=255)
                                                                                            aTAAGGTAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCTGAAAATGAAAAACAACACCAAATc  <  1:289814/100‑1 (MQ=255)
                                                                                                 |                                                                                              
TGCAAACGTCTCTGCGAGACAAAGCCATCATAAAAAACAGGGAGATACGCTTTTTGATAGGAATCAATCAATTACATGAATATAAACTATCAATAAGATAGCCTGTGCCTATTACCCAGATCAGGAATGGCATATCATGATTGCGGCGAGAGCAGGATTGAATGTTCTGAAAATGAAAAACAACACCAAATC  >  NC_000913/3669243‑3669434

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A