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 F17 I0 R2	162	60.6	4616657	98.5%	4547407	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,707,036	G→A	14.5%	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	14.5%	166.9 / 17.7	62	A483T (GCC→ACC)	yieN	fused predicted transcriptional regulators
Reads supporting (aligned to +/- strand): ref base G (30/23); new base A (6/3); total (36/26)
Fisher's exact test for biased strand distribution p-value = 7.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

CAACACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAATGT  >  W3110S.gb/3706967‑3707105

caaCACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagc                                                                      >  1:2067460/1‑71 (MQ=255)

 aaCACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAag                                                                       >  1:3323029/1‑69 (MQ=255)

   cacGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagccag                                                                   >  1:1306414/1‑71 (MQ=255)

    acGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagccagc                                                                  <  1:805502/71‑1 (MQ=255)

      gCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagccagc                                                                  >  1:2166705/1‑69 (MQ=255)

          tATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTa                                                               >  1:4180224/1‑68 (MQ=255)

            ttCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAg                                                            >  1:2789210/1‑69 (MQ=255)

              cAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATg                                                        >  1:1047177/1‑71 (MQ=255)

              cAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATg                                                        >  1:3064267/1‑71 (MQ=255)

               aGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGt                                                       <  1:3509598/71‑1 (MQ=255)

               aGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGt                                                       <  1:2502345/71‑1 (MQ=255)

                 cGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAag                                                                       >  1:1579631/1‑53 (MQ=255)

                   aaCAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGTCGGt                                                   >  1:227255/1‑71 (MQ=255)

                    aCAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACa                                                             >  1:2605789/1‑60 (MQ=255)

                    aCAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTAc                                                              >  1:2504363/1‑59 (MQ=255)

                         aaaaaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAagccag                                                                   >  1:709374/1‑49 (MQ=255)

                          aaaaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGa                                            <  1:133999/71‑1 (MQ=255)

                            aaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGAtt                                          >  1:3610898/1‑71 (MQ=255)

                            aaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGAtt                                          >  1:3605451/1‑71 (MQ=255)

                            aaTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGTCGGTGCACAGAtt                                          >  1:912627/1‑71 (MQ=255)

                             aTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAag                                                                       >  1:1205797/1‑41 (MQ=255)

                             aTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTc                                         >  1:3447593/1‑71 (MQ=255)

                             aTGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTc                                         >  1:1265378/1‑71 (MQ=255)

                               gTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGt                                                       >  1:4490917/1‑55 (MQ=255)

                                tCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGcc                                      <  1:3642575/71‑1 (MQ=255)

                                tCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGcc                                      <  1:1612541/71‑1 (MQ=255)

                                tCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGcc                                      <  1:3166191/71‑1 (MQ=255)

                                 cTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTc                                                      <  1:2786645/54‑1 (MQ=255)

                                 cTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGc                                       >  1:3468302/1‑69 (MQ=255)

                                 cTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGc                                       >  1:2005662/1‑69 (MQ=255)

                                  tGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGAt                                           <  1:4308547/64‑1 (MQ=255)

                                  tGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGTCGGTg                                                  <  1:1649991/57‑1 (MQ=255)

                                        tCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGcaca                               <  1:105044/70‑1 (MQ=255)

                                           cTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCAcaacaa                           >  1:1444277/1‑71 (MQ=255)

                                            tGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTg                                                  <  1:2474197/47‑1 (MQ=255)

                                            tGGCGACTCGTTAGGTCGCATTGAAGCCAGCCTAGAgg                                                           <  1:4183065/38‑1 (MQ=37)

                                             ggCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         >  1:2927809/1‑71 (MQ=255)

                                             ggCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         >  1:449879/1‑71 (MQ=255)

                                             ggCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         >  1:3931852/1‑71 (MQ=255)

                                              gCGACTGGTTAGGTCGCATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAAt                          <  1:1285256/69‑1 (MQ=255)

                                               cGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCt                       <  1:3199012/71‑1 (MQ=255)

                                                gACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         <  1:3329765/68‑1 (MQ=255)

                                                  cTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAAc                    <  1:1206485/71‑1 (MQ=255)

                                                   tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGcac                                <  1:1722925/58‑1 (MQ=255)

                                                   tGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaa                              >  1:4105809/1‑60 (MQ=255)

                                                     gTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATg                         >  1:2693402/1‑63 (MQ=255)

                                                     gTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGc                  <  1:4234065/70‑1 (MQ=255)

                                                      ttAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTc                                         >  1:4571219/1‑46 (MQ=255)

                                                      ttAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACg                   <  1:4170457/68‑1 (MQ=255)

                                                       tAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGcac                                               >  1:653203/1‑39 (MQ=255)

                                                       tAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGcac                                >  1:1049926/1‑54 (MQ=255)

                                                       tAGGTCGCATTGAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTg                >  1:3783727/1‑70 (MQ=255)

                                                        aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGca                                                >  1:4265509/1‑37 (MQ=255)

                                                        aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTgg               <  1:3303508/70‑1 (MQ=255)

                                                        aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTgg               <  1:2411312/70‑1 (MQ=255)

                                                        aGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGa              >  1:4340022/1‑71 (MQ=255)

                                                         ggTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGa              <  1:1400126/70‑1 (MQ=255)

                                                            cGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACg          >  1:2150/1‑71 (MQ=255)

                                                             gCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCt                 >  1:1490706/1‑63 (MQ=255)

                                                             gCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGc         >  1:4610662/1‑71 (MQ=255)

                                                               aTTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACg                   <  1:1674584/59‑1 (MQ=255)

                                                               aTTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCtt       <  1:1565856/71‑1 (MQ=255)

                                                                ttGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTa      <  1:1161854/71‑1 (MQ=255)

                                                                 tGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTaa     >  1:2972801/1‑71 (MQ=255)

                                                                  gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCacaa                              >  1:804659/1‑45 (MQ=255)

                                                                  gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    >  1:2095762/1‑71 (MQ=255)

                                                                  gAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    >  1:2970871/1‑71 (MQ=255)

                                                                  gAAGCAAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTaa     >  1:3690548/1‑70 (MQ=255)

                                                                  gAAACCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    >  1:739070/1‑71 (MQ=255)

                                                                   aaGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAt    <  1:2804877/70‑1 (MQ=255)

                                                                    agccagccTACAGGATGTCGGTGCACAGATTCGCCAg                                    >  1:3442838/1‑37 (MQ=255)

                                                                    agccagccTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAAtgt  <  1:1094275/71‑1 (MQ=255)

                                                                     gccagccTACAGGATGTCGGTGCACAGATTCGCCAGGCacaa                              >  1:845808/1‑42 (MQ=255)

CAACACGCTTTATTCAGCGAACAGCAAAAATGTCTGTTTATCCCTGGCGACTGGTTAGGTCGCATTGAAGCCAGCCTACAGGATGTCGGTGCACAGATTCGCCAGGCACAACAATGCTAACGCTGGATACGCTTAATGT  >  W3110S.gb/3706967‑3707105

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A