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	1,606,349	C→T	30.6%	L23L (CTG→TTG)	hemF →	coproporphyrinogen III oxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,606,349	0	C	T	30.6%	48.7 / 22.1	52	L23L (CTG→TTG)	hemF	coproporphyrinogen III oxidase
Reads supporting (aligned to +/- strand): ref base C (10/26); new base T (9/7); total (19/33)
Fisher's exact test for biased strand distribution p-value = 6.54e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.12e-01

TATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGTTGGCAGCGCGAAGCTGGCGG  >  minE/1606282‑1606407

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:2167927/69‑1 (MQ=255)

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:535753/69‑1 (MQ=255)

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:420518/69‑1 (MQ=255)

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:3012266/69‑1 (MQ=255)

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:3001603/69‑1 (MQ=255)

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:2264820/69‑1 (MQ=255)

tATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:2831933/69‑1 (MQ=255)

 aTGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:3427550/68‑1 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:2874288/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:214746/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:2673159/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:2788716/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:2937224/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:529815/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:68930/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGag                                                        >  1:1101017/1‑68 (MQ=255)

   gAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGTTGa                                                         >  1:218726/1‑68 (MQ=255)

    aaaCCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGAcc                                                       >  1:1463612/1‑69 (MQ=255)

    aaaCCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGAcc                                                       >  1:1479163/1‑69 (MQ=255)

     aaCCCGACGCACACCAGGTTAAACAGTTTCTGCTAAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:1497856/64‑1 (MQ=255)

        ccGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:2540374/61‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:1990320/69‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:3077878/69‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:473145/69‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:3339985/69‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:2613726/69‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:2446807/69‑1 (MQ=255)

          gACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTc                                                 <  1:1858657/69‑1 (MQ=255)

             gCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCt                                                           <  1:149440/56‑1 (MQ=255)

             gCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTg                                                          <  1:1437391/57‑1 (MQ=255)

             gCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTg                                                          <  1:3180417/57‑1 (MQ=255)

                   cAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGAc                                                        >  1:1421117/1‑53 (MQ=255)

                   cAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGgcgc                                         >  1:2942860/1‑68 (MQ=255)

                   cAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGgcgc                                         >  1:346912/1‑68 (MQ=255)

                        tAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACAGCCGTCGATGGCGCAGAAtt                                   >  1:2771584/1‑69 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:3397267/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:423265/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:905357/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:2241739/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:1466675/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:1446572/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGTTGAGCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGCTg                    <  1:1179276/69‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGCTGACCTCCGTCGATGGCGCAGAATTTGTCGAAGATAGtt                     <  1:1231973/68‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGtt                     <  1:2747760/68‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGtt                     <  1:2497679/68‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGtt                     <  1:3410515/68‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGtt                     <  1:1198475/68‑1 (MQ=255)

                                       cAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGta                     <  1:1176521/68‑2 (MQ=255)

                                                         ttGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGTTGGCAGCGCGAAGCTggcgg  >  1:3384354/1‑69 (MQ=255)

                                                         ttGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGTTGGCAGCGCGAAGCTggcgg  >  1:2143619/1‑69 (MQ=255)

                                                         ttGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGTTGGCAGCGCGAAGCTggcgg  >  1:1897824/1‑69 (MQ=255)

                                                         ttGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGTTGGCAGCGCGAAGCTggcg   >  1:3388326/1‑68 (MQ=255)

TATGAAACCCGACGCACACCAGGTTAAACAGTTTCTGCTCAACCTTCAGGATACGATTTGTCAGCAGCTGACCGCCGTCGATGGCGCAGAATTTGTCGAAGATAGTTGGCAGCGCGAAGCTGGCGG  >  minE/1606282‑1606407

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A