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
A3 F2 I1 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	Exported	218,049	C→T	63.4%	N12N (AAC→AAT)	yafF →	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	218,049	0	C	T	63.4%	177.8 / 208.5	213	N12N (AAC→AAT)	yafF	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (42/36); new base T (75/60); total (117/96)
Fisher's exact test for biased strand distribution p-value = 8.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

Only 100 of 215 total aligned reads displayed.

GAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGG  >  Exported/217981‑218119

gagaATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACg                                                                       <  1:890734/70‑1 (MQ=255)

   aaTAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACgcag                                                                    >  1:1359225/1‑70 (MQ=255)

   aaTAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACgcag                                                                    >  1:311949/1‑70 (MQ=255)

     tAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACgcag                                                                    >  1:4570676/1‑68 (MQ=255)

       aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGaa                                                               >  1:183671/1‑71 (MQ=255)

       aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAACGCCGCAGaa                                                               >  1:4182443/1‑71 (MQ=255)

          tGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAACGCCGCAGAatta                                                            >  1:3152724/1‑71 (MQ=255)

             actggCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGcagcag                                                                 <  1:1353206/60‑1 (MQ=255)

             actggCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTAttt                                                         >  1:1553993/4‑71 (MQ=255)

             actggCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAACGCCGCAGAATTAttt                                                         >  1:2476369/4‑71 (MQ=255)

              ctggCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTAtttt                                                        >  1:2305285/3‑71 (MQ=255)

                ggCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAACGCCGCAGAATTAtttt                                                        >  1:56813/1‑69 (MQ=255)

                 gCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAg                                                     >  1:3619865/1‑71 (MQ=255)

                 gCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAg                                                     >  1:671335/1‑71 (MQ=255)

                 gCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAg                                                     >  1:4531804/1‑71 (MQ=255)

                 gCGTCTGGACGTGGTAATGAATGAACACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCa                                                      <  1:3796423/70‑1 (MQ=255)

                  cGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAgg                                                    <  1:3748484/71‑1 (MQ=255)

                    tCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAatta                                                            >  1:2613107/1‑61 (MQ=255)

                     cTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGa                                                  >  1:2518259/1‑70 (MQ=255)

                       ggACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGaa                                                               <  1:3307548/55‑1 (MQ=255)

                        gACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGa                                                  >  1:4419242/1‑67 (MQ=255)

                            tGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGca                                           >  1:1214694/1‑70 (MQ=255)

                             ggTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGcaca                                         >  1:3224214/1‑71 (MQ=255)

                              gTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACAt                                        >  1:5314869/1‑71 (MQ=255)

                              gTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCa                                                      >  1:5633730/1‑57 (MQ=255)

                              gTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACAt                                        >  1:2329927/1‑71 (MQ=255)

                               tattgattgaaGACGACTGCAAAATAAGTAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGcaca                                         <  1:3340743/66‑1 (MQ=255)

                               tAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCa                                                      >  1:171575/1‑56 (MQ=255)

                                aatgaatgAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTAtttt                                                        <  1:1145339/53‑1 (MQ=255)

                                 atgaatgaAGACGACTGCAAAATAAGAAGAGGAAATgcagca                                                                  >  1:2257540/1‑42 (MQ=38)

                                 atgaatgaAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACAtt                                       >  1:2440737/1‑69 (MQ=255)

                                 atgaatgaAGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACAtt                                       >  1:4311200/1‑69 (MQ=255)

                                 atgaatgaAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGc                                     >  1:304137/1‑71 (MQ=255)

                                  ttaatgaaGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGca                                           <  1:5656797/62‑1 (MQ=255)

                                  tgaatgaaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAatt                                                             <  1:1942229/46‑1 (MQ=255)

                                   gaatgaaGACGACTGCAAAATAAGAAGAGGAAACGCCGCAGAATTAtttt                                                        >  1:2553238/1‑50 (MQ=255)

                                   gaatgaaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACgg                                             <  1:715715/61‑1 (MQ=255)

                                    aatgaaGACGACTGCAAAATAAGAAGAGGAAATgca                                                                     >  1:3494624/1‑36 (MQ=37)

                                    aatgaaGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTAt                                  >  1:2615393/1‑71 (MQ=255)

                                    aatgaaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAattat                                                           >  1:5437508/1‑46 (MQ=255)

                                    aatgaaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAg                                                     >  1:4225505/1‑52 (MQ=255)

                                     atgaaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAg                                                     <  1:4952854/51‑1 (MQ=255)

                                      tgaaGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTAtt                                 >  1:1028655/1‑70 (MQ=255)

                                      tgaaGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTAt                                  >  1:3233097/1‑69 (MQ=255)

                                      tgaaGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTAt                                  >  1:4403200/1‑69 (MQ=255)

                                      tgaaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGc                                     <  1:3350386/66‑1 (MQ=255)

                                        aaGACGACTGCAAAATAAGAAGAGGAAATgcagca                                                                  >  1:1258354/1‑35 (MQ=25)

                                        aaGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTaa                               >  1:5394675/1‑70 (MQ=255)

                                        aaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTc                                                       >  1:4097642/1‑46 (MQ=255)

                                        aaGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTaa                               >  1:4932436/1‑70 (MQ=255)

                                         cgacgacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTaa                               <  1:2274405/68‑1 (MQ=255)

                                         acacgacTGCAAAATAAGAAGAGGAAACGCCGCAGAATTAtttt                                                        <  1:5632639/42‑1 (MQ=38)

                                         aGACGACTGCAAAATAAGAAGAGGAAATGcagcag                                                                 <  1:2019559/35‑1 (MQ=25)

                                         aGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTAtttt                                                        <  1:2458371/44‑1 (MQ=38)

                                         aGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTAttt                                                         <  1:4025033/43‑1 (MQ=38)

                                         aGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTAttt                                                         <  1:4744382/43‑1 (MQ=38)

                                         aGACGACTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAgg                                                    <  1:4016282/48‑1 (MQ=38)

                                         aGACGACTGCAAAATAAGAAGAGGAAACGCCGCAGAATTAtttt                                                        <  1:2795275/44‑1 (MQ=38)

                                         aGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAata                             <  1:2389810/71‑1 (MQ=255)

                                          gacgacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGa                                                  <  1:831704/49‑1 (MQ=38)

                                          gacgacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGca                                           <  1:2987679/56‑1 (MQ=255)

                                           acgacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGa                                                  <  1:3765346/48‑1 (MQ=38)

                                           acgacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATAtt                           >  1:450137/1‑71 (MQ=255)

                                            cgacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTAtttt                                                        <  1:3847454/41‑1 (MQ=38)

                                            cgacTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAg                                                     <  1:5622136/44‑1 (MQ=255)

                                             gacTGCAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATAtttt                         >  1:2661568/1‑71 (MQ=255)

                                             gacTACAAAATAAGAAGAGGAAACGCAGCAGAATTAtttt                                                        <  1:149770/40‑1 (MQ=255)

                                             gacTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATAtttt                         <  1:2872822/71‑1 (MQ=255)

                                               ctgcAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGa                       >  1:3547216/4‑71 (MQ=255)

                                               ctgcAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGa                       >  1:5377879/4‑71 (MQ=255)

                                               cTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGAt                                                 >  1:4668912/1‑45 (MQ=255)

                                                 gcAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAgg                                                    <  1:4797169/39‑1 (MQ=38)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAgg                                                    <  1:404943/39‑1 (MQ=255)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATa                                                >  1:3190140/1‑43 (MQ=255)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATa                                                >  1:3687767/1‑43 (MQ=255)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGcaca                                         >  1:114062/1‑50 (MQ=255)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACAtt                                       >  1:4291140/1‑52 (MQ=255)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACg                     >  1:762677/1‑70 (MQ=255)

                                                  cAAAATAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGAACATTGCTATTAATATTTTGa                       >  1:5052829/1‑68 (MQ=255)

                                                  cAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAg                                                     >  1:2926465/1‑38 (MQ=255)

                                                  cAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACg                     >  1:5263405/1‑70 (MQ=255)

                                                   aaaaTAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGa                    <  1:541146/70‑1 (MQ=255)

                                                     aaTAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGca                                           >  1:5569306/1‑45 (MQ=255)

                                                      aTAAGAAGAGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATga                <  1:3439115/71‑1 (MQ=255)

                                                       tAAGAAGAGGAAACGCCGCAGAATTATTTTCAGGGa                                                  >  1:3659104/1‑36 (MQ=255)

                                                         agaagaGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATgata              <  1:222589/70‑3 (MQ=255)

                                                          gaagaGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAg            <  1:3909241/71‑1 (MQ=255)

                                                           aagaGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAgg           <  1:5116099/71‑1 (MQ=255)

                                                            agagGAAACGCAGCAGAATTATTTTCAGGGATACGGc                                            <  1:2917256/37‑1 (MQ=255)

                                                             gagGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAgg           <  1:3475987/69‑1 (MQ=255)

                                                              agGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTAt        <  1:435695/71‑1 (MQ=255)

                                                              agGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTAt        <  1:4482819/71‑1 (MQ=255)

                                                               ggAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAAt                  <  1:553203/60‑1 (MQ=255)

                                                                gAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTAtt       >  1:4751481/1‑70 (MQ=255)

                                                                gAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTc      <  1:930754/71‑1 (MQ=255)

                                                                  aaCGCCGCAGAATTATTTTCAGGGATACGGCACATCGCTATTAATATTTTAACGAATGATAAGGTATTc      >  1:2723863/1‑69 (MQ=255)

                                                                  aaCGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTc      <  1:1627686/69‑1 (MQ=255)

                                                                   aCGCCGCAGAATTATTTTCAGGGATACGGCACATCGCTATTAATATTTTAACg                     <  1:4908362/53‑1 (MQ=38)

                                                                   aCGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTAtt                                 <  1:3705333/41‑1 (MQ=255)

                                                                    cGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAgg  >  1:4587884/1‑71 (MQ=255)

GAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGG  >  Exported/217981‑218119

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