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
A5 F28 I1 R1	108	95.2	3177646	99.2%	3152224	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,410,177	A→G	V15V (GTA→GTG)	yjfI →	conserved protein YjfI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,410,177	0	A	G	98.2%	197.6 / ‑4.4	54	V15V (GTA→GTG)	yjfI	conserved protein YjfI
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (38/15); total (39/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

ACGTATTGCAAATATTCATTTTATTAATATTTAAACTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTACCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGTGAG  >  NC_000913/4410076‑4410311

aCGTATTGCAAATATTCATTTTATTAATATTTAAACTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGc                                                                                                  >  1:768518/1‑140 (MQ=255)

   tATTGCAAATATTCATTTTATTAATATTTAAACTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCatt                                                                                               >  2:629996/1‑140 (MQ=255)

      tGCAAATATTCATTTTATTAATATTTAAACTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCattaat                                                                                            >  1:253544/1‑140 (MQ=255)

                cATTTTATTAATATTTAAACTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAaatg                                                                                  <  1:629996/140‑1 (MQ=255)

                                 aaCTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGAttt                                                                 >  2:604480/1‑140 (MQ=255)

                                       aTCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAAt                                                           >  2:237112/1‑140 (MQ=255)

                                       aTCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAAt                                                           >  2:1192650/1‑140 (MQ=255)

                                             atGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAatat                                                     >  1:778156/1‑140 (MQ=255)

                                                 aataatATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCtt                                                 >  2:973699/1‑140 (MQ=255)

                                                 aataatATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCtt                                                 >  2:1044092/1‑140 (MQ=255)

                                                    aataTATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCttttt                                              >  2:1401087/1‑140 (MQ=255)

                                                      tatatGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTAc                                            >  2:1299586/1‑140 (MQ=255)

                                                      tatatGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTAc                                            >  2:195338/1‑140 (MQ=255)

                                                      tatatGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTAc                                            >  2:1333891/1‑140 (MQ=255)

                                                      tatatGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTAc                                            >  1:798020/1‑140 (MQ=255)

                                                      tatatGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTAc                                            >  1:358609/1‑140 (MQ=255)

                                                        tatGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACtt                                          <  2:768518/140‑1 (MQ=255)

                                                           gACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGTCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTccc                                       >  2:454461/1‑140 (MQ=255)

                                                           gACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTccc                                       >  2:765370/1‑140 (MQ=255)

                                                           gACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTccc                                       >  1:121004/1‑140 (MQ=255)

                                                           gACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTccc                                       >  1:55264/1‑140 (MQ=255)

                                                           gACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTccc                                       >  2:219676/1‑140 (MQ=255)

                                                             cATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGc                                     >  2:693613/1‑140 (MQ=255)

                                                               tGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTACCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCa                                   >  2:897064/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTGTGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:1322512/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  2:1330329/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:1066510/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  2:1536461/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  2:283923/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  2:666971/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  <  1:219676/140‑1 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  2:1306066/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:982615/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:673166/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:1560890/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:958148/1‑140 (MQ=255)

                                                                ggAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCaa                                  >  1:878474/1‑140 (MQ=255)

                                                                      cGTTGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGAtt                            >  2:1520895/1‑140 (MQ=255)

                                                                        ttGGCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTAt                          >  2:1344605/1‑140 (MQ=255)

                                                                          ggCGCTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCg                        <  1:973699/140‑1 (MQ=255)

                                                                              cTAGCGACGGCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAAc                    >  2:1097064/1‑140 (MQ=255)

                                                                                    aCGGCGCTGCAAACTGTGTCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTAt              <  1:454461/140‑1 (MQ=255)

                                                                                      ggCGCTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTAttt            >  2:628429/1‑140 (MQ=255)

                                                                                        cgcTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGt          <  2:121004/140‑1 (MQ=255)

                                                                                        cgcTGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGt          <  2:358609/140‑1 (MQ=255)

                                                                                           tGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCg       >  1:713877/1‑140 (MQ=255)

                                                                                           tGCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCg       <  1:1306066/140‑1 (MQ=255)

                                                                                            gCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCgg      <  2:778156/140‑1 (MQ=255)

                                                                                            gCAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCgg      <  1:283923/140‑1 (MQ=255)

                                                                                             cAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGt     <  1:1299586/140‑1 (MQ=255)

                                                                                             cAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGt     <  2:253544/140‑1 (MQ=255)

                                                                                             cAAACTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGt     <  1:1333891/140‑1 (MQ=255)

                                                                                               aaCTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGTGa   <  1:1401087/140‑1 (MQ=255)

                                                                                                aCTGTGCCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGTGag  <  1:195338/140‑1 (MQ=255)

ACGTATTGCAAATATTCATTTTATTAATATTTAAACTTAATCTATATGGAATAATATATGACATGGAATCCGTTGGCGCTAGCGACGGCGCTGCAAACTGTACCTGAACAAAATATTGATGTAACAAATAGCGAGAACGCATTAATTATTAAAATGAATGATTATGGCGATTTGCAAATCAATATTCTTTTTACTTCCCGCCAAATGATTATCGAAACCTTTATTTGTCCGGTGAG  >  NC_000913/4410076‑4410311

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A