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
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	982,656	G→A	36.0%	T34T (ACG→ACA)	ydfA →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	982,656	0	G	A	36.0%	129.1 / 117.7	129	T34T (ACG→ACA)	ydfA	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (30/52); new base A (23/23); total (53/76)
Fisher's exact test for biased strand distribution p-value = 1.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.99e-01

Only 100 of 133 total aligned reads displayed.

CTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATGGATTTCGACAC  >  minE/982588‑982725

ctGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTAAACCAAAAGCAAAACGtt                                                                     >  1:476508/1‑71 (MQ=255)

 tGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACg                                                                       <  1:3554955/68‑1 (MQ=255)

 tGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACg                                                                       <  1:1984123/68‑1 (MQ=255)

   gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                                                    <  1:2964101/69‑1 (MQ=255)

   gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                                                                  <  1:5040189/71‑1 (MQ=255)

   gtgtGCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTa                                                                   <  1:312039/70‑1 (MQ=255)

   gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                                                  <  1:5059234/71‑1 (MQ=255)

   gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                                                  <  1:3155242/71‑1 (MQ=255)

   gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                                                  <  1:4165288/71‑1 (MQ=255)

   gtgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTa                                                                   <  1:5164881/70‑1 (MQ=255)

    tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                                                                 <  1:4275073/71‑1 (MQ=255)

    tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                                                                 <  1:4568437/71‑1 (MQ=255)

    tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaaa                                                                 <  1:3289837/71‑1 (MQ=255)

    tgtgCGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTaa                                                                  >  1:157976/1‑70 (MQ=255)

    tgtACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaaa                                                                 <  1:5295608/71‑1 (MQ=255)

        cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                                                             <  1:4455141/71‑1 (MQ=255)

        cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                                                             <  1:2057759/71‑1 (MQ=255)

        cGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCg                                                             <  1:2442740/71‑1 (MQ=255)

        cGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAAcc                                                              >  1:591429/1‑70 (MQ=255)

        cGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCg                                                             <  1:2175992/71‑1 (MQ=255)

        cGGCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCg                                                             <  1:1420245/71‑1 (MQ=255)

         ggCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGa                                                            <  1:2237662/71‑1 (MQ=255)

         ggCGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGa                                                            <  1:3707637/71‑1 (MQ=255)

           cGTGTTCCCCAACCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:2098552/1‑71 (MQ=255)

             tgtTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGt                                                                      <  1:3591019/57‑1 (MQ=255)

               tttCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGttt                                                                    >  1:4496144/1‑57 (MQ=255)

                 tCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTaaaa                                                                >  1:3939251/1‑59 (MQ=255)

                   cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGcc                                                  >  1:4718072/1‑71 (MQ=255)

                   cAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGc                                                   <  1:1170512/70‑1 (MQ=255)

                    caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                                                    >  1:1347487/2‑52 (MQ=255)

                    caaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACAttt                                                                    >  1:5544429/2‑52 (MQ=255)

                     aaCCAGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGcgcg                                                <  1:5188924/71‑1 (MQ=255)

                     aaCCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACg                                                                       <  1:2747890/48‑1 (MQ=255)

                         aGGATGGAACGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCga                                            <  1:3247907/71‑2 (MQ=255)

                           gACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                                           <  1:667521/54‑1 (MQ=255)

                            aCGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCgctgg                                         <  1:3627447/71‑1 (MQ=255)

                             cGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaaaa                                                         >  1:4481924/1‑54 (MQ=255)

                             cGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATg                                                       >  1:670407/1‑56 (MQ=255)

                                cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                                           <  1:1800783/49‑1 (MQ=255)

                                cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                                           <  1:1716495/49‑1 (MQ=255)

                                cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                                           <  1:131105/49‑1 (MQ=255)

                                cACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAAt                                                        <  1:724862/52‑1 (MQ=255)

                                aaCGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCGatggttgg                                     <  1:3552788/70‑1 (MQ=255)

                                 aCGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                                           <  1:528210/48‑1 (MQ=255)

                                 aCGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGaa                                                           <  1:1992832/48‑1 (MQ=255)

                                  cGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCgatggttg                                      >  1:3223200/1‑68 (MQ=255)

                                  cGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCgatggttg                                      >  1:5157372/1‑68 (MQ=255)

                                  cGTTCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAAATGGTGCGCGCCgatggttg                                      >  1:3871693/1‑68 (MQ=255)

                                  cGTTCACCGCAATGACGTATACCAATAGCAAAACGTTTAAAACCGAAAATGGTGcc                                                  <  1:8980/56‑1 (MQ=255)

                                    ttCACTGCCATGACGTATACCAAAAGCAAAACAtt                                                                     <  1:3068998/35‑1 (MQ=25)

                                    ttCACTGCCATGACGTATACCAAAAGCAAAACAtt                                                                     <  1:4672390/35‑1 (MQ=25)

                                     tCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:3966570/1‑45 (MQ=38)

                                     tCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:3860180/1‑45 (MQ=38)

                                     tCACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:2965193/1‑45 (MQ=38)

                                      cACTGCCATGACGTATACCAAAAGCAAAACATTTAAAACCGAAACTGGTGCGCGCCGATGGTTGgag                                   >  1:5012133/1‑66 (MQ=255)

                                      cACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaaga                                <  1:4847846/70‑1 (MQ=255)

                                      cACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaaga                                <  1:4180364/70‑1 (MQ=255)

                                       aCCGCAATGACGTATACCAAAAGCAAAACGTTTaaaa                                                                >  1:838545/1‑37 (MQ=255)

                                       aCCGCAATGACGTATACCAAAAGCAAAACGTTTaa                                                                  <  1:1145679/35‑1 (MQ=255)

                                       aCCGCAATGACGTATACCAAAAGCAAAACGTTTAAAAc                                                               >  1:5433123/1‑38 (MQ=255)

                                         ctcAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACt                            >  1:2670830/3‑71 (MQ=255)

                                         cGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTg                                                    <  1:3073809/47‑1 (MQ=255)

                                             aTGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaa                                  <  1:1546652/61‑1 (MQ=255)

                                             aTGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaa                                  <  1:5006571/61‑1 (MQ=255)

                                              tGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAAt                                                        <  1:5265494/38‑1 (MQ=255)

                                              tGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAAt                                                        <  1:2734298/38‑1 (MQ=255)

                                              tGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGgt                       <  1:3351675/71‑1 (MQ=255)

                                              tGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGgt                       <  1:2549657/71‑1 (MQ=255)

                                               gACGTATACCAAAAGCAAAACGTTTAAAACCGaaaa                                                         >  1:2678744/1‑36 (MQ=255)

                                               gACGTATACCAAAAGCAAAACGTTTAAAACCGaaaa                                                         >  1:5386829/1‑36 (MQ=255)

                                               gACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:5089412/1‑35 (MQ=255)

                                               gACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:1021723/1‑35 (MQ=255)

                                               gACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:4588214/1‑35 (MQ=255)

                                               gACGTATACCAAAAGCAAAACATTTAAAACCGaaa                                                          >  1:749032/1‑35 (MQ=255)

                                               gACGTATACCAAAAGCAAAAAGTTTAAAACCGaaa                                                          >  1:492730/1‑35 (MQ=255)

                                                aCGTATACCAAAAGCAAAACGTTTAAAACCGaaaa                                                         >  1:4665001/1‑35 (MQ=255)

                                                aCGTATACCAAAAGCAAAACGTTTAAAACCGaaaa                                                         >  1:811884/1‑35 (MQ=255)

                                                aCGTATACCAAAAGCAAAACGTTTAAAACCGAAAATgg                                                      >  1:2599585/1‑38 (MQ=255)

                                                     taCCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTc                                              <  1:5663943/41‑1 (MQ=255)

                                                     taCCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTc                                              <  1:5434580/41‑1 (MQ=255)

                                                     taCCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTc                                              <  1:3813525/41‑1 (MQ=255)

                                                     taCCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAg                         <  1:1387796/62‑1 (MQ=255)

                                                       ccAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGgtgagtga                 <  1:3495523/68‑1 (MQ=255)

                                                       ccAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGatat              >  1:2952438/1‑71 (MQ=255)

                                                         aaaaGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATg             >  1:1078776/1‑70 (MQ=255)

                                                           aaGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaa                                   <  1:4209019/46‑1 (MQ=255)

                                                           aaGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATGGAt          >  1:4786817/1‑71 (MQ=255)

                                                           aaGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATGGAt          >  1:3058826/1‑71 (MQ=255)

                                                             gCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGgtgag                    >  1:2541855/1‑59 (MQ=255)

                                                             gCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGgtgag                    >  1:4030641/1‑59 (MQ=255)

                                                             gCAAAACATTTAAAACCGAAACTGGTGCGCGCCgatgg                                         <  1:5535686/38‑1 (MQ=16)

                                                             gCAAAACATTTAAAACCGAAACTGGTGCGCGCCgatgg                                         <  1:138582/38‑1 (MQ=16)

                                                              cAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATGGATTTc       >  1:3982701/1‑71 (MQ=255)

                                                               aaaaCGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGatat              <  1:1819954/63‑1 (MQ=255)

                                                               aaaaCGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGatat              <  1:1281384/63‑1 (MQ=255)

                                                                aaaCGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTc                           <  1:4594842/49‑1 (MQ=255)

                                                                 aaCGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaagaaa                              >  1:1557849/1‑45 (MQ=255)

                                                                 aaCGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGgaaaga                                <  1:4373710/43‑1 (MQ=255)

                                                                  aCGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGga                                    >  1:848033/1‑38 (MQ=255)

                                                                   cGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATGGATTTc       <  1:2853523/66‑1 (MQ=255)

CTGGTGTACGGCGTGTTTCCAAACCAGGACGGCACGTTCACCGCAATGACGTATACCAAAAGCAAAACGTTTAAAACCGAAAATGGTGCCCGTCGCTGGCTGGAAAGAAACTCAGGTGAGTGATATGGATTTCGACAC  >  minE/982588‑982725

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