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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	402,439	T→C	31.3%	A108A (GCA→GCG)	rlpA ←	minor lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	402,439	0	T	C	31.3%	55.9 / 31.9	67	A108A (GCA→GCG)	rlpA	minor lipoprotein
Reads supporting (aligned to +/- strand): ref base T (23/23); new base C (10/11); total (33/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTCGGCAT  >  minE/402371‑402503

acGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCt                                                                  >  1:1182645/1‑69 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:290044/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:637922/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:2033016/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:1697393/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:2040457/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:42939/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:3036366/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:3036513/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:3107094/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:1268807/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:1104614/69‑1 (MQ=255)

     cATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:3124410/69‑1 (MQ=255)

      aTTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGt                                                             <  1:1753807/68‑1 (MQ=255)

        tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCa                                                           >  1:1597855/1‑68 (MQ=255)

        tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                                          >  1:1488208/1‑69 (MQ=255)

        tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                                          >  1:1552158/1‑69 (MQ=255)

        tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                                          >  1:488834/1‑69 (MQ=255)

        tCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAg                                                          >  1:1000212/1‑69 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGTGATTGGAAGCGTTGGATGGGCCGCCGt                                                             >  1:2071737/1‑64 (MQ=39)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGt                                                             >  1:3395396/1‑64 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:430022/1‑65 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:3245024/1‑65 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:1359775/1‑65 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:3378078/1‑65 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:2551327/1‑65 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:2402175/1‑65 (MQ=255)

          gCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:578810/1‑65 (MQ=255)

          gCCCGTTAGCCAGCTTAGTGATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTc                                                            >  1:2146022/1‑65 (MQ=255)

                     aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:924781/69‑1 (MQ=255)

                     aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:730776/69‑1 (MQ=255)

                     aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:2703464/69‑1 (MQ=255)

                     aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:2147862/69‑1 (MQ=255)

                     aGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:2316265/69‑1 (MQ=255)

                      ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:482531/68‑1 (MQ=255)

                      ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:2212511/68‑1 (MQ=255)

                      ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:1619540/68‑1 (MQ=255)

                      ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:1337781/68‑1 (MQ=255)

                      ggTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCg                                             <  1:948595/68‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:658763/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:818027/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:1017732/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:614126/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:935301/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:3343576/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:3322893/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:3182526/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:1671126/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:2040722/69‑1 (MQ=255)

                             gATTCTGGCGTAGCTGGGGATTGGAAGCGTTGGATGGGCCGCCGTCAACTGTGTCGGATCGAAAGCTTc                                     <  1:3033369/69‑1 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCtgt                                                      >  1:1716445/1‑42 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCagag                              >  1:2422958/1‑66 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc                           >  1:2946713/1‑69 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc                           >  1:974659/1‑69 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc                           >  1:1062652/1‑69 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc                           >  1:1559347/1‑69 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc                           >  1:3146556/1‑69 (MQ=255)

                                       tAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGcc                           >  1:216056/1‑69 (MQ=255)

                                                  cGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACt                >  1:53299/1‑69 (MQ=255)

                                                  cGGAAGCGGTGGATGGGCTGCCGTCAGCTGTGTCGGGTCGAATGCTTCGCCAGAGGCCGTCAGGTTACt                >  1:2809471/1‑69 (MQ=255)

                                                            ggATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTc       >  1:1919309/1‑68 (MQ=255)

                                                            ggATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTc       >  1:3229073/1‑68 (MQ=255)

                                                            ggATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTc       >  1:154950/1‑68 (MQ=255)

                                                            ggATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTc       >  1:1305503/1‑68 (MQ=255)

                                                            ggATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTc       >  1:2625464/1‑68 (MQ=255)

                                                                  gCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCggg          >  1:638198/1‑59 (MQ=255)

                                                                  gCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTCGGcat  >  1:2477921/1‑67 (MQ=255)

                                                                  gCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTCGGcat  >  1:867767/1‑67 (MQ=255)

ACGATCATTCGCCCGTTAGCCAGGTTAGTGATTCTGGCGTAGCTGGGGATCGGAAGCGTTGGATGGGCTGCCGTCAGCTGTGTCGGATCGAATGCTTCGCCAGAGGCCGTCAGGTTACTGCCGGGTTCGGCAT  >  minE/402371‑402503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A