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	1,008,134	C→T	33.6%	intergenic (‑112/‑132)	ycbX ← / → ycbY	predicted 2Fe‑2S cluster‑containing protein/predicted methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,008,134	0	C	T	33.6%	65.4 / 51.2	57	intergenic (‑112/‑132)	ycbX/ycbY	predicted 2Fe‑2S cluster‑containing protein/predicted methyltransferase
Reads supporting (aligned to +/- strand): ref base C (19/18); new base T (11/8); total (30/27)
Fisher's exact test for biased strand distribution p-value = 7.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

ATGACGCGCTTATTAGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCCGCGCTGT  >  W3110S.gb/1008064‑1008200

atgacGCGCTTATTAGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTc                                                                    <  1:1187843/71‑1 (MQ=255)

   acGCGCTTATTAGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGt                                                                 <  1:4025591/71‑1 (MQ=255)

      cgcTTATTAGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTg                                                              <  1:2778602/71‑1 (MQ=255)

       gcTTATTAGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTgg                                                             <  1:1696985/71‑1 (MQ=255)

          tattaGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTg                                                              >  1:3849804/1‑67 (MQ=255)

           attaGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGcc                                                           <  1:4348167/69‑1 (MQ=255)

               gCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCt                                                         <  1:2708474/67‑1 (MQ=255)

               gCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGt                                                     <  1:2293772/71‑1 (MQ=255)

                 tataATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAg                                                                  >  1:3032136/1‑56 (MQ=255)

                  ataATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTAt                                                  >  1:814029/1‑71 (MQ=255)

                   taATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGt                                                     <  1:5101648/67‑1 (MQ=255)

                     aTGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCt                                               >  1:3184445/1‑71 (MQ=255)

                     aTGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTa                                                   >  1:2102095/1‑67 (MQ=255)

                        cgcAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGttt                                                               >  1:1934880/1‑52 (MQ=255)

                        cgcAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCg                                             >  1:1012922/1‑70 (MQ=255)

                          caacaaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTTTCAGTTTGGCCCTGGGTTATGCTCGaa                                           <  1:3497649/70‑1 (MQ=255)

                          caacaaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGaaa                                          >  1:4151652/1‑71 (MQ=255)

                           aacaaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGt                                                     <  1:430076/59‑1 (MQ=255)

                           aacaaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGaa                                           <  1:1093921/69‑1 (MQ=255)

                           aacaaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGaa                                           <  1:3037335/69‑1 (MQ=255)

                           aacaaTTTTCTTAGCGCCTATCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGaaa                                          >  1:2139169/1‑70 (MQ=37)

                             caaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATcc                                       >  1:2684323/1‑71 (MQ=255)

                             caaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATcc                                       >  1:2329050/1‑71 (MQ=255)

                              aaTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCt                                      <  1:3577178/71‑1 (MQ=255)

                               aTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCt                                      >  1:4260428/1‑70 (MQ=255)

                               aTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAg                                                                  <  1:3921896/42‑1 (MQ=255)

                               aTTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAg                                                                  <  1:4939952/42‑1 (MQ=255)

                                 tttCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCa                                    >  1:3456788/1‑70 (MQ=255)

                                   tCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACg                                  >  1:2320105/1‑70 (MQ=255)

                                   tCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACg                                  >  1:964603/1‑70 (MQ=255)

                                   tCTTAGAGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACg                                  >  1:264/1‑70 (MQ=255)

                                    tttAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGcc                                                           >  1:4215474/2‑44 (MQ=255)

                                    cTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGcc                                                           >  1:827771/1‑44 (MQ=255)

                                    cTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGcc                                                           >  1:821909/1‑44 (MQ=255)

                                    cTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGt                                 <  1:898828/70‑1 (MQ=255)

                                    cTTAGCCCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGcc                                                           >  1:4737610/1‑44 (MQ=255)

                                        gcgcCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACtt                             <  1:779189/70‑1 (MQ=255)

                                          gcCTGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTtgtg                          <  1:3324947/71‑1 (MQ=255)

                                          gcCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTtgtg                          <  1:1669435/71‑1 (MQ=255)

                                          gcCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTtgtg                          <  1:4700520/71‑1 (MQ=255)

                                          gcCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTtgtg                          <  1:2314171/71‑1 (MQ=255)

                                             tGTCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTtgtg                          <  1:421538/68‑1 (MQ=255)

                                               tCCCATTAGGCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTa                        >  1:3353185/1‑68 (MQ=255)

                                                    ttAGGCTATTTTATTTGT‑AGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGt               <  1:2662940/71‑1 (MQ=255)

                                                    ttAGGCTACTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCt                                      <  1:5018745/49‑1 (MQ=255)

                                                      aGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGtt              >  1:2849428/1‑71 (MQ=255)

                                                       ggCTATTTTATTTGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGttt             <  1:2625425/71‑1 (MQ=255)

                                                            ttttatttGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTgtgt                         <  1:465069/54‑1 (MQ=255)

                                                            ttttatttGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCcg        >  1:4578462/1‑71 (MQ=255)

                                                             tttatttGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCcgc       >  1:3101214/1‑71 (MQ=255)

                                                              ttatttGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACg                      >  1:4725798/1‑55 (MQ=255)

                                                              ttatttGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCcgcg      >  1:2982798/1‑71 (MQ=255)

                                                              ttatttGTTAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCcgc       <  1:1694421/70‑1 (MQ=255)

                                                              ttatttGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTAc                       >  1:1872643/1‑54 (MQ=255)

                                                              ttatttGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTAc                       >  1:3550052/1‑54 (MQ=255)

                                                              ttatttGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCcgcg      >  1:1763249/1‑71 (MQ=255)

                                                                   tGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCg                 >  1:1754142/1‑55 (MQ=255)

                                                                    gTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCCGCGCtgt  <  1:2243965/69‑1 (MQ=255)

ATGACGCGCTTATTAGCTATAATGCGCAACAATTTTCTTAGCGCCTGTCCCATTAGGCTATTTTATTTGTCAGTTTGGCCCTGGGTTATGCTCGAAATCCTCACGTACTTGTGTACGCTCCGGTTTCTCCGCGCTGT  >  W3110S.gb/1008064‑1008200

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