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	3,707,036	G→A	23.5%	A483T (GCC→ACC)	yieN →	fused predicted transcriptional regulators

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,707,036	0	G	A	23.5%	138.2 / 38.2	68	A483T (GCC→ACC)	yieN	fused predicted transcriptional regulators
Reads supporting (aligned to +/- strand): ref base G (19/33); new base A (5/11); total (24/44)
Fisher's exact test for biased strand distribution p-value = 7.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

AACACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAATGT  >  W3110S.gb/3706968‑3707105

aaCACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagcc                                                                     <  1:1939112/71‑1 (MQ=255)

aaCACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagc                                                                      >  1:4146358/1‑70 (MQ=255)

aaCACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagc                                                                      >  1:1424005/1‑70 (MQ=255)

 acacGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAaacca                                                                    <  1:3212914/71‑1 (MQ=255)

 acacGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAaacca                                                                    <  1:2025523/71‑1 (MQ=255)

  cacGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagccag                                                                   >  1:4612536/1‑71 (MQ=255)

  cacGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAaaccag                                                                   <  1:489895/71‑1 (MQ=255)

        ttATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTa                                                               >  1:2328297/1‑69 (MQ=255)

         tATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCATCCTAc                                                              <  1:1199023/69‑1 (MQ=255)

         tATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTAc                                                              <  1:4321122/69‑1 (MQ=255)

         tATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTAc                                                              <  1:3789377/69‑1 (MQ=255)

         tATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTAc                                                              <  1:2544411/69‑1 (MQ=255)

          aTTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAg                                                            <  1:877130/70‑1 (MQ=255)

          aTTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAg                                                            <  1:4894389/70‑1 (MQ=255)

          aTTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAg                                                            <  1:3511829/70‑1 (MQ=255)

              aGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGt                                                       <  1:849319/71‑1 (MQ=255)

                cGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGt                                                       <  1:3125713/69‑1 (MQ=255)

                          aaaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCTCATTGAAACCAGCCTACAg                                                            <  1:4652261/54‑1 (MQ=39)

                           aaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACATGATGTCGGTGCACAGAtt                                          <  1:2565015/71‑1 (MQ=255)

                                     tATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGca                                 >  1:4690811/1‑70 (MQ=255)

                                     tATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGca                                 >  1:3769294/1‑70 (MQ=255)

                                     tATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGca                                 >  1:2742281/1‑70 (MQ=255)

                                      aTCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAgg                                                           <  1:2406308/43‑1 (MQ=255)

                                         ccTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaaca                            <  1:3551778/71‑1 (MQ=255)

                                         ccTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaaca                            <  1:4677060/71‑1 (MQ=255)

                                          cTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaaca                            <  1:645443/70‑1 (MQ=255)

                                          cTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCAcaacaa                           <  1:2937372/71‑1 (MQ=255)

                                          cTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCAcaacaa                           <  1:2850625/71‑1 (MQ=255)

                                          cTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCAcaacaa                           <  1:1326746/71‑1 (MQ=255)

                                            ggCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAgg                                   <  1:4418142/61‑1 (MQ=255)

                                            ggCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAAt                          >  1:3009957/1‑70 (MQ=255)

                                            ggCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         >  1:3068769/1‑71 (MQ=255)

                                            ggCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         >  1:878477/1‑71 (MQ=255)

                                             gCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGa                                                          <  1:385378/37‑1 (MQ=255)

                                              cGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:4379660/71‑1 (MQ=255)

                                              cGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:2375854/71‑1 (MQ=255)

                                               gACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATg                                                        >  1:4896627/1‑37 (MQ=255)

                                               gACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATg                                                        >  1:114764/1‑37 (MQ=255)

                                               gACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATg                                                        >  1:3477535/1‑37 (MQ=255)

                                                  tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaac                             <  1:672939/61‑1 (MQ=255)

                                                  tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:2763644/67‑1 (MQ=255)

                                                  tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:4232475/67‑1 (MQ=255)

                                                  tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:3988925/67‑1 (MQ=255)

                                                  tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:2312112/67‑1 (MQ=255)

                                                  tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACg                   >  1:5121445/1‑71 (MQ=255)

                                                    gTTAGGTCGCTTTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCt                 >  1:4054889/1‑71 (MQ=255)

                                                    gTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGGACAACAATGCTAACGCt                 >  1:1456632/1‑71 (MQ=255)

                                                     ttAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCAcaacaa                           >  1:4975021/1‑60 (MQ=255)

                                                       aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTaa                     >  1:2079918/1‑64 (MQ=255)

                                                       aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTa                      <  1:2281457/63‑1 (MQ=255)

                                                       aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTgg               <  1:400604/70‑1 (MQ=255)

                                                        ggTCGCATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGa              <  1:2770047/70‑1 (MQ=255)

                                                         gTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAAc                    >  1:1112526/1‑63 (MQ=255)

                                                            gCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGc         <  1:1363098/71‑1 (MQ=255)

                                                            gCATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGc         >  1:752929/1‑71 (MQ=255)

                                                             cATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCt        <  1:3235824/71‑1 (MQ=255)

                                                              aTTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaac                             <  1:2234463/49‑1 (MQ=255)

                                                              aTTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaac                             <  1:2273583/49‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGcc                                      <  1:741238/39‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGcc                                      <  1:2802643/39‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGcc                                      <  1:642725/39‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAgg                                   <  1:972909/42‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAgg                                   <  1:1450858/42‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAgg                                   <  1:2327806/42‑1 (MQ=255)

                                                               ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCATGCACAACAATGCTAACGCTGGATAc           <  1:3863147/66‑1 (MQ=255)

                                                               ttGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAAc                    <  1:1543528/57‑1 (MQ=255)

                                                               ttGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTa      <  1:4873028/71‑1 (MQ=255)

                                                                tGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTaa     >  1:1435817/1‑71 (MQ=255)

                                                                 gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGc         >  1:1773722/1‑66 (MQ=255)

                                                                 gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTaa     <  1:240417/70‑1 (MQ=255)

                                                                 gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    >  1:2583174/1‑71 (MQ=255)

                                                                 gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    >  1:3666875/1‑71 (MQ=255)

                                                                 gAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTaa                     >  1:2390082/1‑54 (MQ=255)

                                                                 gAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGc         >  1:3923420/1‑66 (MQ=255)

                                                                 gAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    >  1:4917186/1‑71 (MQ=255)

                                                                   agccagccTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAtgt  <  1:1462939/71‑1 (MQ=255)

AACACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAATGT  >  W3110S.gb/3706968‑3707105

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