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 R2	230	93.6	4701257	96.3%	4527310	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,512,673	A→T	54.6%	intergenic (‑144/‑136)	yicE ← / → gltS	predicted transporter/glutamate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,512,673	0	A	T	54.6%	22.4 / 120.0	86	intergenic (‑144/‑136)	yicE/gltS	predicted transporter/glutamate transporter
Reads supporting (aligned to +/- strand): ref base A (22/17); new base T (20/27); total (42/44)
Fisher's exact test for biased strand distribution p-value = 2.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CATCTAAATATTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCATAGTTCAT  >  minE/2512604‑2512742

cATCTAAATATTTAAATGAGATAAATGCACTTTTTTATATGACTTTTGGTATTTTTCTGCTTAAAATCCa                                                                       >  1:1648735/1‑70 (MQ=255)

    tAAATATTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCa                                                                  >  1:4586935/1‑71 (MQ=255)

     aaaTATTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCAt                                                                 >  1:3853005/1‑71 (MQ=255)

      aaTATTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCAtt                                                                <  1:1611543/71‑1 (MQ=255)

      aaTATTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCAtt                                                                <  1:2711248/71‑1 (MQ=255)

        tatTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTg                                                              <  1:3321074/71‑1 (MQ=255)

          tttAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGtt                                                            <  1:4456433/71‑1 (MQ=255)

            tAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCa                                                          >  1:1199697/1‑71 (MQ=255)

             aaaTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCa                                                                       >  1:1615959/1‑57 (MQ=255)

             aaaTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCa                                                          <  1:2160543/70‑1 (MQ=255)

              aaTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCAtt                                                        <  1:494709/71‑1 (MQ=255)

              aaTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCAt                                                         <  1:4316461/70‑1 (MQ=255)

              aaTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCAtt                                                        <  1:2684152/71‑1 (MQ=255)

              aaTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCAt                                                         <  1:2745897/70‑1 (MQ=255)

               aTGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCAtt                                                        >  1:4592892/1‑70 (MQ=255)

                tGAGATAAATGCACTTTTTTATATGACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTaa                                                      >  1:3042049/1‑71 (MQ=255)

                 gagaTAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTaa                                                      >  1:3909544/1‑70 (MQ=255)

                  agaTAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAAc                                                     <  1:2163015/70‑1 (MQ=255)

                   gaTAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAg                                                   >  1:591434/1‑71 (MQ=255)

                         tGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTATAATCCTTGCCATTTGTTCATTAACAGCTgaga                                             <  1:1625002/71‑1 (MQ=255)

                         tGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTgag                                              >  1:815581/1‑70 (MQ=255)

                           cACTTTTTTATATGACTTTTGGTATTTTTCTGCTTAAAATCCATGCCAtt                                                                >  1:252896/1‑50 (MQ=255)

                           cACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAAt                                           >  1:3208040/1‑71 (MQ=255)

                           cACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGaa                                            <  1:2835097/70‑1 (MQ=255)

                              ttttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGtt                                                            <  1:3649302/51‑1 (MQ=255)

                              ttttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTc                                                           <  1:931426/52‑1 (MQ=255)

                               tttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCa                                                          >  1:1459446/1‑52 (MQ=255)

                               tttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCAtt                                                        <  1:1134734/54‑1 (MQ=255)

                               tttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCAtt                                                        <  1:3542465/54‑1 (MQ=255)

                               tttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTc                                                           <  1:3600564/51‑1 (MQ=255)

                               tttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGACATTTGTTCATTAACAGCTGAGAATTTGa                                       >  1:3517959/1‑71 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCa                                                                       >  1:832550/1‑38 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCa                                                                       >  1:1359229/1‑38 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCa                                                          >  1:1088961/1‑51 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAg                                                   >  1:4350981/1‑58 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGAc                                      >  1:3673789/1‑71 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGAc                                      >  1:2205001/1‑71 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGAc                                      >  1:4337450/1‑71 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTga                                               >  1:3484497/1‑62 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGAc                                      >  1:4491418/1‑71 (MQ=255)

                                ttttATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGAc                                      >  1:1381527/1‑71 (MQ=255)

                                 tttATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGAcc                                     >  1:4034309/1‑71 (MQ=255)

                                     tataACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAAttt                                         <  1:3783030/63‑1 (MQ=255)

                                      ataACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGtt                                                            <  1:2335794/43‑1 (MQ=255)

                                      ataACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAgg                                 >  1:3072732/1‑70 (MQ=255)

                                       taACTTTTGGTATTTTTCTGCTTAAACTCCATGCCAtt                                                                <  1:791109/38‑1 (MQ=255)

                                       taACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGaa                               <  1:2177782/71‑1 (MQ=255)

                                       taACTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGa                                <  1:2692330/70‑1 (MQ=255)

                                        aaCTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCa                                                          >  1:1861415/1‑43 (MQ=255)

                                        aaCTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGa                                >  1:4193953/1‑69 (MQ=255)

                                        aaCTTTTGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCAAGGa                                >  1:1150668/1‑69 (MQ=255)

                                        aaCTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGtt                                                            <  1:2265922/41‑1 (MQ=255)

                                         aCTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAg                             >  1:2747531/1‑71 (MQ=255)

                                          cTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAg                             >  1:176121/1‑70 (MQ=255)

                                          cTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGc                            <  1:1347091/71‑1 (MQ=255)

                                             ttGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTga                                               >  1:1102865/1‑49 (MQ=255)

                                             ttGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCAt                          <  1:506715/70‑1 (MQ=255)

                                              tGGTATTTTTCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATa                         <  1:3416297/70‑1 (MQ=255)

                                                gTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAAc                       <  1:1459493/70‑1 (MQ=255)

                                                gTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAAc                       <  1:653431/70‑1 (MQ=255)

                                                gTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACt                      <  1:4170653/71‑1 (MQ=255)

                                                 tATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTc                     <  1:1934904/71‑1 (MQ=255)

                                                   tttttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTgag                                              <  1:3110295/44‑1 (MQ=255)

                                                   tttttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGa                   <  1:3930711/71‑1 (MQ=255)

                                                   tttttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGa                   <  1:486603/71‑1 (MQ=255)

                                                   tttttCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGaa                                            >  1:4586303/1‑46 (MQ=255)

                                                   tttttCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGaa                                            >  1:3583725/1‑46 (MQ=255)

                                                   tttttCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCa                                   >  1:386110/1‑55 (MQ=255)

                                                     tttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAAt                                           >  1:3362777/1‑45 (MQ=255)

                                                     tttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTc                     <  1:3123045/67‑1 (MQ=255)

                                                     tttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGa                   >  1:1062483/1‑69 (MQ=255)

                                                     tttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATa                 >  1:2600223/1‑71 (MQ=255)

                                                     tttCTGCTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATa                 >  1:327558/1‑71 (MQ=255)

                                                     tttCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGa                                       >  1:4296560/1‑49 (MQ=255)

                                                     tttCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATa                 >  1:4655608/1‑71 (MQ=255)

                                                     tttCTGCTTAAAATCCATGCCATTTGTTCAATAACAGCTGAGAATTTGa                                       >  1:1481482/1‑49 (MQ=255)

                                                         tGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCAt                          <  1:2270543/58‑1 (MQ=255)

                                                           cTTAAAATCCTTGCCATTTGTTCATTAAGAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGt            >  1:32551/1‑70 (MQ=255)

                                                           cTTAAAATCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGt            <  1:3460858/70‑1 (MQ=255)

                                                            ttAAAATCCTTGCCATTTGTTCATTAACTGCTGAGAATTTGACCCa                                   <  1:4523474/46‑1 (MQ=39)

                                                            ttAAAATCCTTGCCATTTGTTCATTAACAGCTgaga                                             <  1:864960/36‑1 (MQ=255)

                                                              aaaaTCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGt            <  1:2078541/67‑1 (MQ=255)

                                                              aaaaTCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCa          <  1:2621259/69‑1 (MQ=255)

                                                              aaaaTCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCAt         <  1:4316959/70‑1 (MQ=255)

                                                              aaaaTCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCAt         <  1:410537/70‑1 (MQ=255)

                                                               aaaTCCTTGCCATTTGTTCATTAACAGCAGAGAATTTGAccc                                    >  1:3231925/1‑42 (MQ=255)

                                                                 aTCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTc                     <  1:577890/55‑1 (MQ=255)

                                                                  tCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCATAg       >  1:92981/1‑68 (MQ=255)

                                                                  tCCTTGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCATAGTTc    <  1:4287098/71‑1 (MQ=255)

                                                                    cATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCATAGTTCAt  >  1:2584858/1‑71 (MQ=255)

CATCTAAATATTTAAATGAGATAAATGCACTTTTTTATATAACTTTTGGTATTTTTCTGCTTAAAATCCATGCCATTTGTTCATTAACAGCTGAGAATTTGACCCAGGAAAGCATAACTCGATACCCGTCATAGTTCAT  >  minE/2512604‑2512742

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A