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	2,086,906	T→C	57.9%	H227H (CAT→CAC)	yqjG →	predicted S‑transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,086,906	0	T	C	57.9%	21.6 / 45.3	64	H227H (CAT→CAC)	yqjG	predicted S‑transferase
Reads supporting (aligned to +/- strand): ref base T (14/13); new base C (16/21); total (30/34)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACTACGCTGGTGCG  >  minE/2086840‑2086968

ttACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATc                                                               >  1:2263092/1‑68 (MQ=255)

ttACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATc                                                               >  1:2268366/1‑68 (MQ=255)

ttACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATc                                                               >  1:2570840/1‑68 (MQ=255)

ttACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATc                                                               >  1:2482359/1‑68 (MQ=255)

ttACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATc                                                               >  1:358267/1‑68 (MQ=255)

ttACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATc                                                               >  1:1800903/1‑68 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTa                                                           <  1:2107965/68‑1 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTa                                                           <  1:2038609/68‑1 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTa                                                           <  1:1824154/68‑1 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:1800644/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:3240772/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:1692510/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:1551505/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:1547892/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:1504772/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:724597/1‑69 (MQ=255)

    gacgaGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTAc                                                          >  1:123991/1‑69 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:366354/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:639723/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:24715/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:2391327/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:337538/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:1393137/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:783654/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:2239759/69‑1 (MQ=255)

             gTGGCGAAAGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGc                                                 <  1:2574738/69‑1 (MQ=255)

               ggCGAAAGTGTTTGAATCGCTGGCACGACTCGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCaa                                               <  1:3276427/69‑1 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCa                                            >  1:845534/1‑67 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:3072137/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:3352757/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:3357949/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:3404085/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:351842/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:366492/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:2595199/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:519403/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:1118078/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:2541444/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:2588373/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:1010921/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:1327848/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:1766405/1‑68 (MQ=255)

                    aaGTGTTTAAATCGCTGGCGCGACTGGAACAGATTTTAGGTCAGCACCGTTACCTGACCGGCAACCAg                                           >  1:180907/1‑68 (MQ=255)

                             aaTCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGaa                                  <  1:930283/68‑1 (MQ=255)

                             aaTCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGaa                                  <  1:851755/68‑1 (MQ=255)

                             aaTCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGaa                                  <  1:2104850/68‑1 (MQ=255)

                                 gCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGa                             <  1:2030927/69‑1 (MQ=255)

                                 gCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGa                             <  1:1931762/69‑1 (MQ=255)

                                 gCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGa                             <  1:1309153/69‑1 (MQ=255)

                                 gCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGa                             <  1:1394879/69‑1 (MQ=255)

                                 gCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGa                             <  1:473901/69‑1 (MQ=255)

                                 gCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCCGCAACCAGCTAACCGAAGCCGa                             <  1:3099656/69‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:2755820/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:3301912/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:2906345/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:2256787/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:38267/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:1463582/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:2255797/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:2167842/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:1924548/68‑1 (MQ=255)

                                                            tcAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:210253/68‑1 (MQ=255)

                                                             cAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:1452654/68‑1 (MQ=255)

                                                             cAGCACCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACCACGCTGGTGCg  <  1:667833/68‑1 (MQ=255)

TTACGACGAGGCGGTGGCGAAAGTGTTTGAATCGCTGGCACGACTGGAGCAGATTTTAGGCCAGCATCGTTACCTGACCGGCAACCAGCTAACCGAAGCCGATATTCGCCTGTGGACTACGCTGGTGCG  >  minE/2086840‑2086968

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