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
A8 F1 I1 R1	82	28.6	1225488	97.4%	1193625	116.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,481,904	(A)_8→9	coding (273/1539 nt)	emrY ←	putative multidrug efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,481,896	1	.	A	97.3%	124.4 / ‑3.2	37	coding (281/1539 nt)	emrY	putative multidrug efflux system
Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (22/14); total (22/15)
Fisher's exact test for biased strand distribution p-value = 4.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.08e-01

CTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCG‑‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATG  >  NC_000913/2481765‑2482028

cTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCG‑‑aaaaaaa                                                                                                                               <  2:290652/139‑1 (MQ=255)

cTGGCGGATAATCCCTTAATAATAAACTCTGTGACAGTGGAATTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCG‑‑aaaaaaa                                                                                                                               <  1:55184/139‑1 (MQ=255)

          aTTCCTTAATAATCAACCCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGa                                                                                                                      <  2:380688/139‑1 (MQ=255)

                taataataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTaa                                                                                                                >  1:268279/1‑139 (MQ=255)

                 aataataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTaaa                                                                                                               >  1:172052/1‑139 (MQ=255)

                     ataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAaata                                                                                                           >  1:332379/1‑139 (MQ=255)

                             tgtgACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTaa                                                                                                    >  2:527391/1‑138 (MQ=255)

                             tgtgACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTaa                                                                                                    <  1:527391/138‑1 (MQ=255)

                             tgtgACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAAt                                                                                                   >  2:304664/1‑139 (MQ=255)

                              gtgACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAAtt                                                                                                  >  2:430283/1‑139 (MQ=255)

                                     tGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTAt                                                                                           >  1:209445/1‑139 (MQ=255)

                                     tGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTAt                                                                                           >  1:3287/1‑139 (MQ=255)

                                                  cccGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAAGTCGCCTATTCTTTGTGCCAAc                                                                              >  2:359417/1‑139 (MQ=255)

                                                          tAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGt                                                                      <  2:575856/139‑1 (MQ=255)

                                                                 tGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAggg                                                               >  1:114684/1‑139 (MQ=255)

                                                                       aCTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCa                                                         <  2:332379/139‑1 (MQ=255)

                                                                       aCTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCa                                                         <  2:209445/139‑1 (MQ=255)

                                                                        ctctAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCa                                                         >  2:592706/1‑139 (MQ=255)

                                                                        ctctAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAAcc                                                                             >  1:3955/1‑118 (MQ=255)

                                                                        ctctAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAAcc                                                                             <  2:3955/118‑1 (MQ=255)

                                                                             aaaaaTATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCa                                                   <  1:323251/139‑1 (MQ=255)

                                                                              aaaaTATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCG‑‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCAtt                                                 <  2:104695/139‑1 (MQ=255)

                                                                                             cAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACg                                   <  2:268279/139‑1 (MQ=255)

                                                                                             cAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACg                                   >  2:106161/1‑139 (MQ=255)

                                                                                                   tGGTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGa                             <  2:114684/139‑1 (MQ=255)

                                                                                                    ggTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTaaaaa                                                                                                             >  2:288340/1‑58 (MQ=255)

                                                                                                    ggTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTaaaaa                                                                                                             <  1:288340/58‑1 (MQ=255)

                                                                                                    ggTCGATAGGCTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTAAACCAAACGAGGTGAt                            >  2:220464/1‑139 (MQ=255)

                                                                                                           agaatACACATTAAAGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCATCCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCATACGAGGTGATAACCCAg                     <  1:220464/135‑1 (MQ=255)

                                                                                                              cTACACATTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTg                  >  2:255501/1‑139 (MQ=255)

                                                                                                               tACACATTAATGAAGACAGCGAAAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTg                  <  1:592706/139‑1 (MQ=255)

                                                                                                                 cacaTTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCt               >  1:177547/1‑139 (MQ=255)

                                                                                                                    aTTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGc                                              <  1:460314/105‑1 (MQ=255)

                                                                                                                    aTTAATGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGc                                              >  2:460314/1‑105 (MQ=255)

                                                                                                                        aTGAAGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTg        >  1:562080/1‑139 (MQ=255)

                                                                                                                           aaGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGAt                            >  2:120811/1‑116 (MQ=255)

                                                                                                                           aaGACAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGAt                            <  1:120811/116‑1 (MQ=255)

                                                                                                                              aCAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATg  >  1:295650/1‑139 (MQ=255)

                                                                                                                              aCAGCGA‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATg  >  1:549765/1‑139 (MQ=255)

CTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCG‑‑AAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATG  >  NC_000913/2481765‑2482028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A