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	4,586,637	G→A	34.8%	P365L (CCG→CTG)	hsdM ←	DNA methylase M

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,586,637	0	G	A	34.8%	76.9 / 65.3	69	P365L (CCG→CTG)	hsdM	DNA methylase M
Reads supporting (aligned to +/- strand): ref base G (28/17); new base A (13/11); total (41/28)
Fisher's exact test for biased strand distribution p-value = 6.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.60e-01

AACTCGGCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTAAAAAATACC  >  W3110S.gb/4586572‑4586704

aaCTCGGCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCgg                                                                    >  1:3582133/1‑67 (MQ=255)

aaCTCGGCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCgg                                                                    >  1:4653978/1‑67 (MQ=255)

 aCTCGGCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCg                                                               <  1:4912403/71‑1 (MQ=255)

 aCTCGGCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCg                                                               >  1:1834276/1‑71 (MQ=255)

     ggCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCa                                                            <  1:2556296/70‑1 (MQ=255)

           ttGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTccc                                                     >  1:2629339/1‑71 (MQ=255)

           ttGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTccc                                                     >  1:4175894/1‑71 (MQ=255)

            tGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCt                                                    >  1:3235673/1‑71 (MQ=255)

            tGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCt                                                    >  1:738177/1‑71 (MQ=255)

                   cAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTa                                              >  1:1603936/1‑70 (MQ=255)

                   cAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTaa                                             <  1:2305695/71‑1 (MQ=255)

                   cAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTaa                                             <  1:799171/71‑1 (MQ=255)

                        cATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCa                                                            >  1:1124216/1‑51 (MQ=255)

                         aTACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAAc                                        <  1:72323/70‑1 (MQ=255)

                          tACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAg                                      <  1:3969979/71‑1 (MQ=255)

                            cacCCACACATCATCGGTACAGTTCTTATCCTGATTCAGGTTCGc                                                              >  1:65355/1‑45 (MQ=255)

                            cacCCACACATCATCGGTACAGTTCTTATCCTGATTCAGGTTCGc                                                              >  1:1095307/1‑45 (MQ=255)

                            cacCCACACATCATCGGTACAGTTCTTATCCTGATTCAGGTTCGc                                                              >  1:3795101/1‑45 (MQ=255)

                            cacCCACACATCATCGGTACAGTTCTTATCCTGATTCAGGTTCGCCAc                                                           >  1:4039201/1‑48 (MQ=255)

                            cacCCACACATCATCGGAACAGTTCTTATCCTGATTCAGGTTCGCCAc                                                           >  1:1433207/1‑48 (MQ=255)

                                cacacaTCATCGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCg                                                         >  1:97529/1‑46 (MQ=255)

                                cacacaTCATCGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGtt                                >  1:1283748/1‑71 (MQ=255)

                                 acacaTCATCGGTACAGTTCTTATCCTGATTCAGGTTCCCCACCGTCCCTTTGGTAAAGAACAGCACGTTg                               <  1:4658663/71‑1 (MQ=255)

                                      tcatcGGTACAGTTCTTATCCTGATTCGGGTTCGcc                                                             <  1:4604059/36‑1 (MQ=255)

                                      tcatcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          >  1:2569411/1‑71 (MQ=255)

                                      tcatcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:132240/71‑1 (MQ=255)

                                      tcatcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          >  1:1133870/1‑71 (MQ=255)

                                      tcatcGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:4505239/71‑1 (MQ=255)

                                      tcatcGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:829261/71‑1 (MQ=255)

                                        atcGGTACAGTTCTTATCCTGATTCGGGTTCGCCAc                                                           >  1:4473494/1‑36 (MQ=255)

                                        atcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGaa                                         >  1:4018984/1‑54 (MQ=255)

                                        atcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGaa                                         >  1:1027697/1‑54 (MQ=255)

                                        atcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:5126505/69‑1 (MQ=255)

                                        atcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCa                        >  1:1074794/1‑71 (MQ=255)

                                        atcGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCa                        >  1:1177925/1‑71 (MQ=255)

                                         tcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTa                                              <  1:1878511/48‑1 (MQ=255)

                                         tcGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTa                                              <  1:2794226/48‑1 (MQ=255)

                                         tcGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:2287904/68‑1 (MQ=255)

                                         tcGGTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:2423123/68‑1 (MQ=255)

                                          cGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGaa                                         >  1:2481884/1‑52 (MQ=255)

                                           ggTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCa                        >  1:4866289/1‑68 (MQ=255)

                                           ggTACAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCa                        >  1:474815/1‑68 (MQ=255)

                                              aCAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTaaa                                            >  1:368942/1‑45 (MQ=255)

                                               cAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTg                               >  1:4022583/1‑57 (MQ=255)

                                               cAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTg                               >  1:2078649/1‑57 (MQ=255)

                                               cAGTTCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACg                                  >  1:2375998/1‑54 (MQ=255)

                                                 gTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:4161094/60‑1 (MQ=255)

                                                 gTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:3279766/60‑1 (MQ=255)

                                                 gTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCtt                          <  1:3298740/60‑1 (MQ=255)

                                                  ttCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCa                                    <  1:4284334/49‑1 (MQ=255)

                                                  ttCTTATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGc              <  1:2904121/71‑1 (MQ=255)

                                                    cTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCg             >  1:3239035/1‑70 (MQ=255)

                                                    cTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCg             >  1:1404383/1‑70 (MQ=255)

                                                    cTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCg             >  1:1519158/1‑70 (MQ=255)

                                                     ttATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACg                                  <  1:3644381/48‑1 (MQ=255)

                                                     ttATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACg                                  <  1:852461/48‑1 (MQ=255)

                                                      tATCCTGATTCGGGTTCGCCACCGTCCCTTTGTTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTa           >  1:1892321/1‑70 (MQ=255)

                                                      tATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTa           >  1:4269570/1‑70 (MQ=255)

                                                      tATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCa                        >  1:1834310/1‑57 (MQ=255)

                                                      tATCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCa                        >  1:3771089/1‑57 (MQ=255)

                                                       aTCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAg                                           <  1:4273277/37‑1 (MQ=255)

                                                       aTCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTa           <  1:902255/69‑1 (MQ=255)

                                                        tCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTaaa         >  1:2985948/1‑70 (MQ=255)

                                                        tCCTGATTCAGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTaaaa        <  1:3030267/71‑1 (MQ=255)

                                                        accTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCACTGAGCGTaaa         >  1:3920967/2‑70 (MQ=255)

                                                              ttCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCAc                                   <  1:1344483/38‑1 (MQ=255)

                                                              ttCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCAc                                   <  1:1241665/38‑1 (MQ=255)

                                                              ttCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTAAAAAATAcc  >  1:4479708/1‑71 (MQ=255)

                                                              ttCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTAAAAAATAc   >  1:3435226/1‑70 (MQ=255)

                                                                cGGGTTCGCGACCGTCCCTTTGGTAAAGAACAGCACg                                  >  1:4619213/1‑37 (MQ=255)

                                                                cGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACg                                  >  1:342312/1‑37 (MQ=255)

AACTCGGCATATTGGTACGCAGGTCATACACCCACACATCATCGGTACAGTTCTTATCCTGATTCGGGTTCGCCACCGTCCCTTTGGTAAAGAACAGCACGTTGGTCTTCACGCCCTGAGCGTAAAAAATACC  >  W3110S.gb/4586572‑4586704

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