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 F8 I0 R2	296	77.6	4260404	88.1%	3753415	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,803,598	T→C	27.0%	N30N (AAT→AAC)	ygaH →	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,803,598	0	T	C	27.0%	101.8 / 45.7	63	N30N (AAT→AAC)	ygaH	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base T (35/11); new base C (12/5); total (47/16)
Fisher's exact test for biased strand distribution p-value = 7.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTTGGGTTACTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGATATG  >  minE/1803529‑1803663

gctTGGGTTACTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATg                                                                  >  1:2813094/1‑71 (MQ=255)

 ctTGGGTTACTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAAt                                                                   <  1:2367399/69‑1 (MQ=255)

 ctTGGGTTACTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATgc                                                                 >  1:2618832/1‑71 (MQ=255)

 ctTGGGTTACTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATgc                                                                 >  1:3278993/1‑71 (MQ=255)

         aCTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCccaa                                                         >  1:3681226/1‑71 (MQ=255)

         aCTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCccaa                                                         >  1:1777868/1‑71 (MQ=255)

         aCTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCcca                                                          <  1:2671389/70‑1 (MQ=255)

         aCTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACCCCCGCcca                                                          <  1:2176575/70‑1 (MQ=255)

            aGTTGGGATGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCccaacc                                                       >  1:2413408/1‑70 (MQ=255)

            aGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCccaacc                                                       >  1:1396472/1‑70 (MQ=255)

            aGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCccaacc                                                       >  1:624338/1‑70 (MQ=255)

            aGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCccaacc                                                       >  1:769973/1‑70 (MQ=255)

             gTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCccaacca                                                      <  1:453338/70‑1 (MQ=255)

                   gtggcgAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAAt                                                                   >  1:761994/1‑51 (MQ=255)

                   gtggcgAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTgg                                               >  1:2717712/1‑71 (MQ=255)

                      gcgAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGgcgc                                            >  1:2397331/1‑71 (MQ=255)

                          attattGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCCCAACCAAACGTGGCGCgg                                          >  1:1466156/1‑69 (MQ=255)

                          attattGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCCCAACCAAACGTGGCGCgg                                          >  1:2673749/1‑69 (MQ=255)

                           ttattGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggt                                         <  1:2601977/69‑1 (MQ=255)

                             attGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggtagg                                      >  1:230516/1‑70 (MQ=255)

                             attGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggtagg                                      >  1:1002209/1‑70 (MQ=255)

                             attGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggtagg                                      >  1:1279984/1‑70 (MQ=255)

                             attGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggtag                                       >  1:635644/1‑69 (MQ=255)

                             attGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggtag                                       >  1:3388354/1‑69 (MQ=255)

                             attGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCggtag                                       >  1:1863819/1‑69 (MQ=255)

                                 cTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  <  1:526515/70‑1 (MQ=255)

                                 cTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  <  1:2270925/70‑1 (MQ=255)

                                 cTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  <  1:3842258/70‑1 (MQ=255)

                                    ccGCTATTTGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTg                               <  1:1634657/70‑1 (MQ=255)

                                            tGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGacac                       <  1:3373903/70‑1 (MQ=255)

                                            tGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCccaaccaa                                                     >  1:1004964/1‑40 (MQ=255)

                                            tGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCCCAACCAAACGTg                                                >  1:411160/1‑45 (MQ=255)

                                            tGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCCCAACCAAACGTg                                                >  1:1915537/1‑45 (MQ=255)

                                            tGCCGCTGCGCCTGCGTGTGGGTAACGCCCGCCCAACCAAACGTg                                                >  1:2040933/1‑45 (MQ=255)

                                                 cTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGac                         >  1:3944930/1‑63 (MQ=255)

                                                 cTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGac                         >  1:2741128/1‑63 (MQ=255)

                                                 cTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGac                         >  1:2387401/1‑63 (MQ=255)

                                                 cTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGac                         >  1:2310830/1‑63 (MQ=255)

                                                   gcgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCa               >  1:1218422/1‑71 (MQ=255)

                                                   gcgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCa               >  1:3155571/1‑71 (MQ=255)

                                                   gcgcCTGCGTGTGGGTAATGCCCGCCCAACAAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCa               >  1:2782356/1‑71 (MQ=255)

                                                   gcgcCTGCGTGTGGGTAATGCCCGCACAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCa               >  1:341284/1‑71 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  >  1:3372409/1‑51 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  >  1:3731772/1‑51 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  >  1:207673/1‑51 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  >  1:3029468/1‑51 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  >  1:1112967/1‑51 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTAtt                                  >  1:812034/1‑51 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGc                <  1:2628314/69‑1 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGc                <  1:651178/69‑1 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACAATTGGc                <  1:2709/69‑1 (MQ=255)

                                                    cgcCTGCGTGTGGGTAATGCACGCCCAAGCAAACGTGGCGCGGTAGGTAtt                                  >  1:3278535/1‑51 (MQ=255)

                                                         gCGTGTTGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCAACACCATTGGCATCTCCt         >  1:2413179/1‑71 (MQ=255)

                                                             gtgGGTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGa      >  1:380168/1‑70 (MQ=255)

                                                              tgGGTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGata    <  1:3660349/71‑1 (MQ=255)

                                                              tgGGTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGata    <  1:686216/71‑1 (MQ=255)

                                                               gggTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGata    >  1:3652976/1‑70 (MQ=255)

                                                                ggTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGatat   >  1:1477631/1‑70 (MQ=255)

                                                                ggTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGatat   >  1:2991361/1‑70 (MQ=255)

                                                                ggTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGATATg  >  1:251361/1‑71 (MQ=255)

                                                                ggTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGATATg  >  1:2507629/1‑71 (MQ=255)

                                                                 gTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGATATg  >  1:1379595/1‑70 (MQ=255)

                                                                 gTAACGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGATATg  >  1:2911837/1‑70 (MQ=255)

                                                                  tAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCa                     <  1:1375398/50‑1 (MQ=255)

                                                                  tAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCa                     <  1:1061006/50‑1 (MQ=255)

GCTTGGGTTACTAGTTGGCGTGGCGAATTATTGCTTCCGCTATTTGCCGCTGCGCCTGCGTGTGGGTAATGCCCGCCCAACCAAACGTGGCGCGGTAGGTATTTTGCTCGACACCATTGGCATCGCCTCGATATG  >  minE/1803529‑1803663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A