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
A5 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,199,872	T→C	39.5%	intergenic (‑58/‑400)	ymfE ← / → lit	predicted inner membrane protein/cell death peptidase, inhibitor of T4 late gene expression

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,199,872	0	T	C	39.5%	58.5 / 101.8	86	intergenic (‑58/‑400)	ymfE/lit	predicted inner membrane protein/cell death peptidase, inhibitor of T4 late gene expression
Reads supporting (aligned to +/- strand): ref base T (25/27); new base C (14/20); total (39/47)
Fisher's exact test for biased strand distribution p-value = 6.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

CATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATAT  >  W3110S.gb/1199803‑1199939

cATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtt                                                                    <  1:2959452/71‑1 (MQ=255)

cATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtt                                                                    <  1:3737675/71‑1 (MQ=255)

 atatTATTCACCTTAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACttt                                                                   >  1:2346673/1‑71 (MQ=255)

  tattatTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtttt                                                                  <  1:494911/71‑1 (MQ=255)

  tattatTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtttt                                                                  <  1:2334156/71‑1 (MQ=255)

    ttattCACCTGAGTTACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTc                                                                 <  1:1273848/70‑1 (MQ=255)

      attCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCa                                                                >  1:3642712/1‑69 (MQ=255)

      attCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAg                                                               >  1:3959826/1‑70 (MQ=255)

      attCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAg                                                               <  1:1974344/70‑1 (MQ=255)

       ttCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAg                                                               >  1:4221532/1‑69 (MQ=255)

         cACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAg                                                            <  1:2405683/70‑1 (MQ=255)

           ccTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgtt                                                         <  1:283892/71‑1 (MQ=255)

           ccTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGgtt                                                         <  1:494648/71‑1 (MQ=255)

            cTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTa                                                             >  1:2907/1‑66 (MQ=255)

            cTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTa                                                             >  1:1925922/1‑66 (MQ=255)

                gTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACtttt                                                                  <  1:4178145/57‑1 (MQ=255)

                   aCGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACaa                                                 <  1:2311458/71‑1 (MQ=255)

                   aCGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACaa                                                 >  1:376220/1‑71 (MQ=255)

                    cGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAt                                                >  1:4163533/1‑71 (MQ=255)

                    cGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAt                                                >  1:3022498/1‑71 (MQ=255)

                      cTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAttt                                              <  1:4514864/71‑1 (MQ=255)

                      cTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAttt                                              <  1:2889698/71‑1 (MQ=255)

                       tttAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCa                                                                <  1:1031731/52‑1 (MQ=255)

                        ttAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgt                                                          <  1:4724395/57‑1 (MQ=255)

                        ttAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGgt                                                          <  1:2185079/57‑1 (MQ=255)

                        ttAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGgtta                                                        >  1:2078304/1‑59 (MQ=255)

                         tAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGt                                                              >  1:4269017/1‑52 (MQ=255)

                         tAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGt                                                              >  1:1597515/1‑52 (MQ=255)

                                gtgtAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTg                                    <  1:522986/71‑1 (MQ=255)

                                gtgtAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTg                                    <  1:3643253/71‑1 (MQ=255)

                                gtgtAATGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTg                                    <  1:1395529/71‑1 (MQ=255)

                                   tAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGtt                                  <  1:2838135/70‑1 (MQ=255)

                                     aTGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCa                                <  1:2340545/70‑1 (MQ=255)

                                     aTGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAg                               >  1:4311295/1‑71 (MQ=255)

                                     aTGGTAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCa                                <  1:2612042/70‑1 (MQ=255)

                                      tGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAgg                              <  1:3287012/71‑1 (MQ=255)

                                        gTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCt                            <  1:1494683/71‑1 (MQ=255)

                                        gTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCt                            <  1:1895204/71‑1 (MQ=255)

                                         tAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:4695373/71‑1 (MQ=255)

                                         tAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:4446475/71‑1 (MQ=255)

                                         tAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:834169/71‑1 (MQ=255)

                                         tAATATTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:4732443/71‑1 (MQ=255)

                                          aaTATTTAATTAAGTGTCATTATATACTTTTCAGTa                                                             <  1:15401/36‑1 (MQ=255)

                                            tatTTAATTAAGTGTCATTATATACCTTTCAGTAGgttagt                                                      <  1:3813778/41‑1 (MQ=255)

                                            tatTTAATTAAGTGTCATTATATACCTTTCAGTAGgttagt                                                      <  1:4057177/41‑1 (MQ=255)

                                            tatTTAATTAAGTGTCATTATATACCTTTCAGTAGgttagt                                                      <  1:3766188/41‑1 (MQ=255)

                                             atTTAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGAcc                        >  1:1878226/1‑70 (MQ=255)

                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATc                                      <  1:411216/55‑1 (MQ=255)

                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATc                                      <  1:3909725/55‑1 (MQ=255)

                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATc                                      <  1:2387570/55‑1 (MQ=255)

                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGAcc                        >  1:1278355/1‑69 (MQ=255)

                                              tttAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGAcc                        >  1:808079/1‑69 (MQ=255)

                                              tttAATTAAGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGAcc                        >  1:4396839/1‑69 (MQ=255)

                                                taattaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTa                                        >  1:3655318/1‑51 (MQ=255)

                                                taattaaGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAg                     <  1:2447725/70‑1 (MQ=255)

                                                taattaaGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAg                     <  1:5009256/70‑1 (MQ=255)

                                                taattaaGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTACCTGTTCAGGCTGACCTAg                     >  1:1504110/1‑70 (MQ=255)

                                                 aattaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAAttttt                                            >  1:1335791/1‑46 (MQ=255)

                                                  attaaGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCtt                  <  1:4908771/71‑1 (MQ=255)

                                                   ttaaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTc                 <  1:4104515/71‑1 (MQ=255)

                                                    taaGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:3329387/60‑1 (MQ=255)

                                                     aaGTGTCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGc               >  1:3102540/1‑71 (MQ=255)

                                                       gtgtCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTg             <  1:3213792/71‑1 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGtt                                  <  1:1199660/47‑1 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGtt                                  <  1:5110797/47‑1 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGtt                                  <  1:1580632/47‑1 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgaca          <  1:4553315/71‑1 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgaca          <  1:1074850/71‑1 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTga            >  1:4100132/1‑69 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTga            >  1:3744096/1‑69 (MQ=255)

                                                          tCATTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTga            >  1:630604/1‑69 (MQ=255)

                                                            aTTATATACTTTTCAGTAGGTTAGTTACAAttttt                                            >  1:1030554/1‑35 (MQ=255)

                                                            aTTATATACTTTTCAGTAGGTTAGTTACAAttttt                                            >  1:2285394/1‑35 (MQ=255)

                                                            aTTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCa                                >  1:199150/1‑47 (MQ=255)

                                                            aTTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgacaga        >  1:3818975/1‑71 (MQ=255)

                                                            aTTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgacaga        >  1:3667787/1‑71 (MQ=255)

                                                            aTTATATACCTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgaca          >  1:3403705/1‑69 (MQ=255)

                                                             ttATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgacagac       <  1:2243141/71‑1 (MQ=255)

                                                                tataCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACaa     >  1:2138897/1‑70 (MQ=255)

                                                                tataCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACaa     >  1:5119547/1‑70 (MQ=255)

                                                                tataCTTTTCAGTAGGTTAGTTACAATTTTTTGCATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACaa     <  1:2621722/70‑1 (MQ=255)

                                                                  taCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:3590566/46‑1 (MQ=255)

                                                                  taCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:4842345/46‑1 (MQ=255)

                                                                  taCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTg                           <  1:279280/46‑1 (MQ=255)

                                                                  taCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAatat  >  1:4183635/1‑71 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTg                                    >  1:2992619/1‑36 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTg                                    >  1:4419258/1‑36 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTgac           >  1:4572206/1‑61 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTga            >  1:4940982/1‑60 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTga            >  1:1495272/1‑60 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAata   >  1:4840029/1‑69 (MQ=255)

                                                                   aCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAata   >  1:3425642/1‑69 (MQ=255)

CATATTATTCACCTGAGTCACGCTTTAGGATAGTGTAATGGTAATATTTAATTAAGTGTCATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATAT  >  W3110S.gb/1199803‑1199939

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