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
A1 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,008,583	C→T	67.1%	Q253* (CAA→TAA)	yhiJ →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,008,583	0	C	T	67.1%	100.2 / 79.6	85	Q253* (CAA→TAA)	yhiJ	hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (11/17); new base T (44/13); total (55/30)
Fisher's exact test for biased strand distribution p-value = 1.38e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGA  >  W3110S.gb/4008516‑4008644

ccTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTaa                                                             <  1:727566/70‑1 (MQ=255)

ccTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTaa                                                             <  1:2838562/70‑1 (MQ=255)

ccTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTaa                                                             <  1:3260262/70‑1 (MQ=255)

        aGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAacac                                                     >  1:2839387/1‑70 (MQ=255)

         gTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTaa                                                             <  1:3518101/61‑1 (MQ=255)

           tGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAAt                                                 >  1:288689/1‑71 (MQ=255)

            gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAaca                                                      >  1:2393547/1‑65 (MQ=255)

            gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAaca                                                      >  1:3368098/1‑65 (MQ=255)

            gCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATg                                                >  1:1649952/1‑71 (MQ=255)

               tAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                              >  1:2118386/1‑70 (MQ=255)

                aaTATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTaa                                            >  1:1317253/1‑71 (MQ=255)

                aaTATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTaa                                            >  1:3635234/1‑71 (MQ=255)

                aaTATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTaa                                            >  1:2632944/1‑71 (MQ=255)

                aaTATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTaa                                            >  1:1519149/1‑71 (MQ=255)

                      gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAAc                                                            >  1:2921202/1‑49 (MQ=255)

                      gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAAc                                                            >  1:3288864/1‑49 (MQ=255)

                      gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAAc                                                            >  1:1359169/1‑49 (MQ=255)

                      gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAAc                                                            >  1:1024976/1‑49 (MQ=255)

                      gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaa                                       >  1:1926473/1‑70 (MQ=255)

                      gaagaTGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACaa                                       >  1:955748/1‑70 (MQ=255)

                            gAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAg                                >  1:576419/1‑71 (MQ=255)

                             aaGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAg                                <  1:1920686/70‑1 (MQ=255)

                             aaGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAg                                <  1:1183996/70‑1 (MQ=255)

                             aaGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAg                                <  1:3624526/70‑1 (MQ=255)

                               gTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTa                              >  1:2043598/1‑70 (MQ=255)

                                  ctcAGCGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCt                          >  1:3329838/1‑71 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATcc                           >  1:1186041/1‑70 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATcc                           >  1:1753128/1‑70 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATcc                           >  1:2503488/1‑70 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATcc                           >  1:2433386/1‑70 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATcc                           >  1:1466611/1‑70 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCt                          >  1:1101364/1‑71 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCt                          >  1:361858/1‑71 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCt                          >  1:2403622/1‑71 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCt                          >  1:1567193/1‑71 (MQ=255)

                                  ctcAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCt                          >  1:2936277/1‑71 (MQ=255)

                                    cAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTa                              >  1:529581/1‑65 (MQ=255)

                                    cAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTa                              >  1:458947/1‑65 (MQ=255)

                                     aaCGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaat                                      >  1:2179007/1‑56 (MQ=255)

                                     aaCGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaat                                      >  1:1188705/1‑56 (MQ=255)

                                     aaCGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaat                                      >  1:1284576/1‑56 (MQ=255)

                                     aaCGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                       >  1:3567758/1‑71 (MQ=255)

                                     aaCGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                       >  1:1572802/1‑71 (MQ=255)

                                       cGTATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                       >  1:626771/1‑69 (MQ=255)

                                         ttttGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                              <  1:3276960/42‑1 (MQ=255)

                                         tATTGCTAAGGGAGAACTTTAATGAGTAACTTGACACTAATGTTAATACAATAATCAGTATCCTGAACag                    >  1:1193874/1‑70 (MQ=255)

                                         tATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                    >  1:3117081/1‑70 (MQ=255)

                                         tATTGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACag                    >  1:3689720/1‑70 (MQ=255)

                                         tATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                              <  1:3244989/44‑1 (MQ=255)

                                         tATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                              <  1:2535953/44‑1 (MQ=255)

                                         tATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                              <  1:3264916/44‑1 (MQ=255)

                                         tATTCCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGtt                                              <  1:2608313/44‑1 (MQ=255)

                                           ttGCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTaa                                            >  1:1473041/1‑44 (MQ=255)

                                             gCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaa                  >  1:1166373/1‑68 (MQ=255)

                                             gCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaa                  >  1:787049/1‑68 (MQ=255)

                                             gCTAAGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACagaa                  >  1:742985/1‑68 (MQ=255)

                                                 aGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaa                                       <  1:644769/43‑1 (MQ=255)

                                                 aGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaa                                       <  1:1941810/43‑1 (MQ=255)

                                                 aGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaa                                       <  1:1543427/43‑1 (MQ=255)

                                                 aGGGAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACat           >  1:3718011/1‑71 (MQ=255)

                                                 aGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACat           <  1:447495/71‑1 (MQ=255)

                                                 aGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACat           <  1:3702642/71‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:3231487/50‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:1203895/50‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:1441581/50‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:253581/50‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:87224/50‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:890101/50‑1 (MQ=255)

                                                  gggAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGt                               <  1:1888707/50‑1 (MQ=255)

                                                   ggAGAACTTTAATGAGTAACTTAACACTAATGTTAATACaata                                     >  1:3565508/1‑43 (MQ=255)

                                                   ggAGAACTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACatta         >  1:3249627/1‑71 (MQ=255)

                                                    gagaACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACattat        >  1:266740/1‑71 (MQ=255)

                                                      gaACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACattatt       >  1:83994/1‑70 (MQ=255)

                                                      gaACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACattatt       >  1:1024621/1‑70 (MQ=255)

                                                         cTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTAt                             >  1:3521886/1‑45 (MQ=255)

                                                         cTTTAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTAt                             >  1:459790/1‑45 (MQ=255)

                                                          tttAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                         <  1:103176/48‑1 (MQ=255)

                                                          tttAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                         <  1:1450371/48‑1 (MQ=255)

                                                          tttAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                         <  1:2319025/48‑1 (MQ=255)

                                                            tAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                       >  1:2736867/1‑48 (MQ=255)

                                                            tAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                       >  1:2214823/1‑48 (MQ=255)

                                                            tAATGAGTAACTTAACACTAATGTTAATACAATAATCAGTATCCTGaa                       >  1:2118182/1‑48 (MQ=255)

                                                            tAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGa  <  1:3249296/69‑1 (MQ=255)

                                                            tAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGa  <  1:3088708/69‑1 (MQ=255)

                                                            tAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGa  <  1:2200172/69‑1 (MQ=255)

                                                                   cAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                         <  1:3480650/39‑1 (MQ=255)

                                                                   cAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                         <  1:3383054/39‑1 (MQ=255)

                                                                   cAACTTAACACTAATGTTAATACAATAATCAGTATCCTg                         <  1:2229593/39‑1 (MQ=255)

CCTTAGCCAGTTGCTTAATATAGAAGATGAAGTTCTCAACGTATTGCTAAGGGAGAACTTTAATGAGCAACTTAACACTAATGTTAATACAATAATCAGTATCCTGAACAGAAGAGACATTATTTTAGA  >  W3110S.gb/4008516‑4008644

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