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	2,056,988	G→T	43.2%	intergenic (‑19/‑188)	ygiP ← / → ttdA	predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,056,988	0	G	T	43.2%	56.8 / 91.3	97	intergenic (‑19/‑188)	ygiP/ttdA	predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand): ref base G (31/24); new base T (33/9); total (64/33)
Fisher's exact test for biased strand distribution p-value = 3.04e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

Only 100 of 113 total aligned reads displayed.

AGTACCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTT  >  minE/2056929‑2057055

aGTACCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAg                                                              >  1:1549559/1‑67 (MQ=255)

   aCCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:3258980/1‑69 (MQ=255)

   aCCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:414826/1‑69 (MQ=255)

    ccggCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:1461144/4‑68 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTtgt                                                                    <  1:2505322/57‑1 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTtgt                                                                    <  1:2869782/57‑1 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTtgt                                                                    <  1:2877699/57‑1 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTtgt                                                                    <  1:1450936/57‑1 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTtgt                                                                    <  1:338178/57‑1 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:3135451/1‑68 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:1408458/1‑68 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:1432148/1‑68 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:432169/1‑68 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAg                                                         >  1:2734788/1‑68 (MQ=255)

    ccTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCACAGTTGTGATAAGCGCAg                                                         >  1:216265/1‑68 (MQ=255)

      tGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAgtg                                                       <  1:2633653/68‑1 (MQ=255)

      tGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAgtg                                                       <  1:2935571/68‑1 (MQ=255)

      tGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAgtg                                                       <  1:3226647/68‑1 (MQ=255)

        cAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAgtg                                                       <  1:3069527/66‑1 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:911046/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:2170635/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:191921/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:19586/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:2646763/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1332569/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1689183/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:3156213/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1587609/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:719552/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:631452/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:3287434/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1493956/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1395340/1‑55 (MQ=255)

          aGTCTTTGGCTAAAGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:332612/1‑55 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTc                                                 >  1:2277216/1‑67 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:2630042/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:2475109/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:2916518/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:911117/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:243493/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:2354766/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:1024297/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:1867474/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:1833263/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:1589184/1‑68 (MQ=255)

             cTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCg                                                >  1:1314476/1‑68 (MQ=255)

                tGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAgtg                                                       <  1:2718946/58‑1 (MQ=255)

                   cTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAAc                                          <  1:2140227/68‑1 (MQ=255)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCTCAGTTTTGATa                                                                >  1:2223660/1‑42 (MQ=19)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGa                                                                  >  1:589638/1‑40 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1262652/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1546923/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1584688/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1222206/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1596635/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:2928530/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:861696/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1087991/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:1013039/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:2222231/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:214300/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:2391528/1‑42 (MQ=25)

                       aGGCCAGCTATTTAGCATTGTTAAATATCCGCAGTTTTGATa                                                                >  1:2397417/1‑42 (MQ=25)

                        ggCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGc                                     <  1:872957/68‑1 (MQ=255)

                          ccAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCAt                                  <  1:2863073/69‑1 (MQ=255)

                          ccAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCAt                                  <  1:1213295/69‑1 (MQ=255)

                              cTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTccc                              >  1:295553/1‑69 (MQ=255)

                                aTTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCaa                                             <  1:2477070/52‑1 (MQ=255)

                                aTTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCaa                                             <  1:2429600/52‑1 (MQ=255)

                                aTTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCaa                                             <  1:2990339/52‑1 (MQ=255)

                                   cAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:2979373/1‑67 (MQ=255)

                                   cAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:1137221/1‑67 (MQ=255)

                                   cAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:2024634/1‑67 (MQ=255)

                                   cAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:1749196/1‑67 (MQ=255)

                                   cAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:3274257/1‑67 (MQ=255)

                                   cAGCATCGTTAATTATACGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:1830290/1‑67 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:2333444/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:332219/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:582700/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:895403/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:2384178/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:3286369/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:3179734/65‑1 (MQ=255)

                                       attgTTAAATATCCGCAGTTTTGATAAACGCAGTGTATTTCGCAAAACATTACCATTCCCTGCTCTgg                      <  1:2101702/65‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:3319143/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:279398/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:2012497/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:879177/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:2093961/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:820944/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:708768/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:3123858/69‑1 (MQ=255)

                                                       aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:2454133/69‑1 (MQ=255)

                                                          tgtgATAATCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa     <  1:2848149/66‑1 (MQ=255)

                                                          tgtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGc                           >  1:2436673/1‑44 (MQ=255)

                                                          tgtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAttt  >  1:1205797/1‑69 (MQ=255)

                                                          tgtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAttt  >  1:1820713/1‑69 (MQ=255)

                                                          tgtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAttt  >  1:3059758/1‑69 (MQ=255)

                                                          tgtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAttt  >  1:1813683/1‑69 (MQ=255)

                                                          tgtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAttt  >  1:2924058/1‑69 (MQ=255)

AGTACCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTT  >  minE/2056929‑2057055

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