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 F25 I0 R2 821 102.6 3645220 97.9% 3568670 140.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,170,282 C→G 13.8% W31C (TGG→TGC)  ldtC ← L,D‑transpeptidase linking Lpp to murein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,170,2820CG13.8% 133.0 / 12.8 45W31C (TGG→TGC) ldtCL,D‑transpeptidase linking Lpp to murein
Reads supporting (aligned to +/- strand):  ref base C (16/22);  new base G (3/3);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.32e-01

GTAAGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATAAGCCTGAATTAT  >  NC_000913/1170135‑1170429
                                                                                                                                                    |                                                                                                                                                   
gTAAGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGcc                                                                                                                                                    >  4:463028/1‑149 (MQ=255)
gTAAGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGc                                                                                                                                                     <  1:334807/148‑1 (MQ=255)
 tAAGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCCGACGACTGCCCGCTGGCGGCAGCGGTCa                                                                                                                                                   <  3:112557/149‑1 (MQ=255)
  aaGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAg                                                                                                                                                  >  3:636782/1‑149 (MQ=255)
  aaGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAg                                                                                                                                                  >  4:327415/1‑149 (MQ=255)
    ggATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAgg                                                                                                                                                 >  2:57456/1‑148 (MQ=255)
         aaCGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTgg                                                                                                                                           <  4:373801/149‑1 (MQ=255)
         aaCGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTgg                                                                                                                                           >  3:67981/1‑149 (MQ=255)
         aaCGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTgg                                                                                                                                           >  4:396301/1‑149 (MQ=255)
          aCGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTGATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTgg                                                                                                                                           >  2:431226/1‑148 (MQ=255)
                     aGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGt                                                                                                                                <  1:429320/148‑1 (MQ=255)
                     aGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTa                                                                                                                               <  3:210166/149‑1 (MQ=255)
                                gagCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTagcgccagcgcc                                                                                                                    >  3:885336/1‑149 (MQ=255)
                                    gagaAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTGATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACg                                                                                                                 <  1:431226/148‑1 (MQ=255)
                                    gagaAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACgg                                                                                                                <  3:396301/149‑1 (MQ=255)
                                                               gATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGc                                                                                      <  1:518308/148‑1 (MQ=255)
                                                                aTGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGcc                                                                                     <  2:63669/148‑1 (MQ=255)
                                                                  ggCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGc                                                                                  >  3:661845/1‑149 (MQ=255)
                                                                   gCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTGTTTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAg                                                                                   >  2:7076/1‑148 (MQ=255)
                                                                     ttCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCgag                                                                               >  3:639548/1‑149 (MQ=255)
                                                                           agaACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGaaaaa                                                                          <  1:57456/148‑1 (MQ=255)
                                                                                 accGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGttt                                                                   <  4:254755/149‑1 (MQ=255)
                                                                                    gTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGa                                                                <  4:639548/149‑1 (MQ=255)
                                                                                     tCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGat                                                               <  4:636782/149‑1 (MQ=255)
                                                                                        ttttCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGatca                                                             >  1:149248/1‑148 (MQ=255)
                                                                                          ttCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGAtcatca                                                          <  4:885336/149‑1 (MQ=255)
                                                                                                   aTGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAAt                                                  <  1:912588/148‑1 (MQ=255)
                                                                                                    tGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATc                                                 >  2:755055/1‑148 (MQ=255)
                                                                                                     gAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCacaacccc                                                <  2:149248/148‑5 (MQ=255)
                                                                                                     gAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATcc                                                <  1:650502/148‑1 (MQ=255)
                                                                                                     gAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATcc                                                <  1:755055/148‑1 (MQ=255)
                                                                                                          ttG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCataat                                           >  2:365889/1‑148 (MQ=255)
                                                                                                          ttG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCataat                                           >  1:780976/1‑148 (MQ=255)
                                                                                                                  cGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATaa                                   <  3:463028/149‑1 (MQ=255)
                                                                                                                   gCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAg                                  <  4:67981/149‑1 (MQ=255)
                                                                                                                          caacaccTGGCCGCTGCCGCCAGCGGGCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTg                           >  4:826173/7‑149 (MQ=255)
                                                                                                                               acTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGtaat                       >  1:263399/1‑148 (MQ=255)
                                                                                                                                 tggccGCTGCCGCCAGCGGGCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGtaataa                     >  1:100954/4‑148 (MQ=255)
                                                                                                                                 tGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGtaataa                     <  1:365889/148‑1 (MQ=255)
                                                                                                                                  ggccGCTGCCGCCAGCGGGCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTg                                                                 <  1:841049/101‑1 (MQ=255)
                                                                                                                                  ggccGCTGCCGCCAGCGGGCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTg                                                                 >  2:841049/3‑103 (MQ=255)
                                                                                                                                   cccGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACa                  <  3:94713/149‑1 (MQ=255)
                                                                                                                                      gCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGAt               <  3:327415/149‑1 (MQ=255)
                                                                                                                                       ctgccgccAGCGGGCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATa              <  3:826173/142‑1 (MQ=255)
                                                                                                                                        tgccgccAGCGGGCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATa              <  2:100954/142‑1 (MQ=255)
                                                                                                                                          gcggcAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATAAg            <  2:630346/148‑1 (MQ=255)
                                                                                                                                                   gCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATAAGCCTGAATTa   >  2:163394/1‑148 (MQ=255)
                                                                                                                                                    ccAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATAAGCCTGAATTat  >  2:433547/1‑148 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
GTAAGGATCAACGCCGGGGTTAGCCTGTAACAGAGCGAGAAAGCCGACGTTGTATTTTTTGGCGATGGCTTCCAGAGAACCACCGTCATTTTCCACCACATGAAATTTG‑TTTTCGCCAACCAGACGACTGCCCGCTGGCGGCAGCGGCCAGGTGTTGGCTTTTGCCGGTAGCGCCAGCGCCACGGCAGCGGCGAACGTAAAAAACGTTAGCCAGCGAGAAAAACGCGTTTTGATCATCACCAAAAATCCATAATAAATATAAGGTTATTGTAATAAACAGATAAGCCTGAATTAT  >  NC_000913/1170135‑1170429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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