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
A14 F999 I0 R1	96	52.5	3964927	95.8%	3798400	49.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,948,805	(G)_6→7	coding (1165/1521 nt)	yifB ←	putative magnesium chelatase YifB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,948,799	1	.	G	97.1%	125.4 / ‑2.3	34	coding (1171/1521 nt)	yifB	putative magnesium chelatase YifB
Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (15/18); total (15/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

AACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCGA  >  NC_000913/3948752‑3948843

aaCGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑gg                                            >  1:774569/1‑50 (MQ=255)

aaCGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑gg                                            >  1:2376904/1‑50 (MQ=255)

aaCGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑g                                             <  1:1256780/49‑1 (MQ=255)

   ggTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑ggggg                                         >  1:284146/1‑50 (MQ=255)

    gTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑gggggg                                        >  1:608333/1‑50 (MQ=255)

      ggCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑gggggggt                                      >  1:970581/1‑48 (MQ=255)

       gcgcTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑gggggggt                                      <  1:2491345/49‑3 (MQ=255)

           tgctTTCTCCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTaa                                  >  1:1459266/1‑50 (MQ=255)

            gctTTCTCCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAAt                                 >  1:994940/1‑50 (MQ=255)

             ctTTCTCCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAAt                                 <  1:1627897/49‑1 (MQ=255)

              tttCTCCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATgg                               >  1:1670556/1‑50 (MQ=255)

              tttCTCCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGGGGTAATgg                               >  1:1617013/1‑50 (MQ=255)

                 ctcCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGa                             <  1:3896243/49‑1 (MQ=255)

                 ctcCCGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGa                             <  1:3857281/49‑1 (MQ=255)

                    ccGGCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGAt                            <  1:3080960/47‑1 (MQ=255)

                      ggCACTACCGTTTTACTCAAAATGCCGGGGGGGGTGGTAATGGGAtctc                         >  1:3083534/1‑49 (MQ=255)

                      ggCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCa                       <  1:2787387/50‑1 (MQ=255)

                       gCACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAg                      <  1:2778319/50‑1 (MQ=255)

                        cACTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGt                     <  1:2042181/50‑1 (MQ=255)

                         aCTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGt                     >  1:2407821/1‑49 (MQ=255)

                          cTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTga                   <  1:1815065/50‑1 (MQ=255)

                          cTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTga                   <  1:3337169/50‑1 (MQ=255)

                          cTACCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTga                   <  1:1993758/50‑1 (MQ=255)

                           caCCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGt                     >  1:873373/2‑47 (MQ=255)

                            aCCGTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTga                   >  1:1971715/1‑48 (MQ=255)

                               gTTTTACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGAt              <  1:2990878/50‑1 (MQ=255)

                                ttttACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTga                   >  1:429375/1‑44 (MQ=255)

                                ttttACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATc             <  1:3503519/50‑1 (MQ=255)

                                ttttACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATc             <  1:3828756/50‑1 (MQ=255)

                                ttttACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATc             <  1:3552507/50‑1 (MQ=255)

                                 tttACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATc             >  1:1849763/1‑49 (MQ=255)

                                  ttACTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCg            <  1:1148398/49‑1 (MQ=255)

                                     cTCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGc        <  1:1835175/50‑1 (MQ=255)

                                      tCAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCg       >  1:782431/1‑50 (MQ=255)

                                       cAAAATGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCgg      >  1:1474121/1‑50 (MQ=255)

                                        aaaaTGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGt     >  1:408131/1‑50 (MQ=255)

                                        aaaaTGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGt     >  1:510957/1‑50 (MQ=255)

                                        aaaaTGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGt     <  1:1362566/50‑1 (MQ=255)

                                         aaaTGCCG‑GGGGGGTGGCAATGGGATCTCCAGTGAGAGATCGAAGCGGTc    >  1:872555/1‑50 (MQ=255)

                                         aaaTGCC‑‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCg   <  1:3122890/50‑1 (MQ=255)

                                           aTGCCG‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCga  <  1:2425210/50‑1 (MQ=255)

AACGGTGGCGCTGCTTTCTCCCGGCACTACCGTTTTACTCAAAATGCC‑‑GGGGGGTGGTAATGGGATCTCCAGTGAGAGATCGAAGCGGTCGA  >  NC_000913/3948752‑3948843

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A