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	1,094,567	T→C	58.7%	I604V (ATT→GTT)	ydiJ ←	predicted FAD‑linked oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,094,567	0	T	C	58.7%	27.7 / 53.9	46	I604V (ATT→GTT)	ydiJ	predicted FAD‑linked oxidoreductase
Reads supporting (aligned to +/- strand): ref base T (7/12); new base C (13/14); total (20/26)
Fisher's exact test for biased strand distribution p-value = 5.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

CCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATAAAC  >  minE/1094513‑1094632

ccAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCgg                                                               >  1:2987610/1‑59 (MQ=255)

ccAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCgg                                                               >  1:1288365/1‑59 (MQ=255)

  aacaaACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCtt                                                 <  1:619404/71‑1 (MQ=255)

   acaaACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGtt                                                             <  1:299608/58‑1 (MQ=255)

   acaaACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCAGGGTGATCTTc                                                <  1:1350786/71‑1 (MQ=255)

   acaaACGCAGCCATTCACGCACAAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTc                                                <  1:1385204/71‑1 (MQ=255)

        cGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGa                                           >  1:2068314/1‑71 (MQ=255)

        cGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGa                                           >  1:1831217/1‑71 (MQ=255)

                ttCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATc                                             <  1:1715451/61‑1 (MQ=255)

                ttCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATc                                             <  1:2310988/61‑1 (MQ=255)

                ttCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATc                                             <  1:4111489/61‑1 (MQ=255)

                ttCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATc                                             <  1:3759282/61‑1 (MQ=255)

                ttCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATc                                             <  1:2457393/61‑1 (MQ=255)

                  cACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATc                                 >  1:3063318/1‑71 (MQ=255)

                  cACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCg                                                                >  1:3476512/1‑40 (MQ=255)

                  cACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGAcaca                                   >  1:3330596/1‑69 (MQ=255)

                  cACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATc                                 >  1:988042/1‑71 (MQ=255)

                  cACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATc                                 >  1:2695489/1‑71 (MQ=255)

                  cACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATc                                 >  1:1930398/1‑71 (MQ=255)

                   aCGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCg                                <  1:987502/71‑1 (MQ=255)

                   aCGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCg                                <  1:1043946/71‑1 (MQ=255)

                   aCGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCg                                <  1:3278789/71‑1 (MQ=255)

                    cGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCgg                               <  1:693064/71‑1 (MQ=255)

                          aGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGaca                                     >  1:2183669/1‑59 (MQ=255)

                          aGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGaca                                     >  1:2311025/1‑59 (MQ=255)

                          aGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGaca                                     >  1:1007217/1‑59 (MQ=255)

                          aGCGTTGCGCGCCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACg                         >  1:3172069/1‑71 (MQ=255)

                              ttGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGAc                             <  1:1850321/63‑1 (MQ=255)

                               tGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCAt                    >  1:1473482/1‑71 (MQ=255)

                                gcgcgcCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCtt                                                 >  1:3289881/1‑41 (MQ=255)

                                gcgcgcCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCtt                                                 >  1:3924130/1‑41 (MQ=255)

                                gcgcgcCCTTTCGGTGAATGAACCCGGTTCTGGGTGATCtt                                                 >  1:2781713/1‑41 (MQ=255)

                                 cgcgcCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCtt                                                 <  1:521392/40‑1 (MQ=255)

                                       cTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTg            <  1:3566231/71‑1 (MQ=255)

                                       cTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTg            <  1:200068/71‑1 (MQ=255)

                                       cTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTg            <  1:1130707/71‑1 (MQ=255)

                                       cTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTg            <  1:1034554/71‑1 (MQ=255)

                                       cTTTCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTg            <  1:1115144/71‑1 (MQ=255)

                                        tttCGGTGAATGAATCCGTTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCaa                 <  1:2371882/65‑1 (MQ=255)

                                        tttCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCaa                 <  1:2539130/65‑1 (MQ=255)

                                        tttCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCaa                 <  1:2426644/65‑1 (MQ=255)

                                        tttCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCaa                 <  1:3699167/65‑1 (MQ=255)

                                        tttCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCaa                 <  1:573325/65‑1 (MQ=255)

                                        tttCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTg            >  1:1858858/1‑70 (MQ=255)

                                          tCGGTGAATGAACCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAg         >  1:788396/1‑71 (MQ=255)

                                            ggTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCa       <  1:2508514/71‑1 (MQ=255)

                                                aatgaatCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATaaa   <  1:2867156/71‑1 (MQ=255)

                                                aatgaatCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATaaa   <  1:2143892/71‑1 (MQ=255)

                                                aatgaacCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATaa    <  1:806690/70‑1 (MQ=255)

                                                aatgaacCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATaa    <  1:938608/70‑1 (MQ=255)

                                                 atgaatCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATaaa   <  1:3110028/70‑1 (MQ=255)

                                                 atgaatCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATAAAc  <  1:455473/71‑1 (MQ=255)

CCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCAAAGTTGAAGCATAAAC  >  minE/1094513‑1094632

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