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 R1	311	50.1	4085234	95.9%	3917739	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,989,906	A→G	30.4%	intergenic (+250/‑18)	ygeF → / → ygeG	hypothetical protein/predicted chaperone

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,989,906	0	A	G	30.4%	150.2 / 95.8	112	intergenic (+250/‑18)	ygeF/ygeG	hypothetical protein/predicted chaperone
Reads supporting (aligned to +/- strand): ref base A (37/41); new base G (17/17); total (54/58)
Fisher's exact test for biased strand distribution p-value = 8.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01

Only 100 of 121 total aligned reads displayed.

CATAATTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCAAATC  >  W3110S.gb/2989838‑2989975

cATAATTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGAcaca                                                                     >  1:695487/1‑71 (MQ=255)

cATAATTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGAcaca                                                                     >  1:1755067/1‑71 (MQ=255)

 aTAATTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGacac                                                                      <  1:854978/69‑1 (MQ=255)

 aTAATTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCAt                                                                    <  1:3072800/71‑1 (MQ=255)

   aaTTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATca                                                                  >  1:1358447/1‑71 (MQ=255)

     tttAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATcaca                                                                <  1:2678955/71‑1 (MQ=255)

       tAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATcaca                                                                >  1:2816393/1‑69 (MQ=255)

         aaaaaGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACag                                                               <  1:2622229/68‑1 (MQ=255)

              gATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAatat                                                       <  1:3593165/71‑1 (MQ=255)

                 aaaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAAtattat                                                    >  1:3680939/1‑71 (MQ=255)

                 aaaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCAAGAGACGCATCACAGAGGAAtattat                                                    >  1:2571867/1‑71 (MQ=255)

                  aaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGaa                                                          <  1:4018339/64‑1 (MQ=255)

                  aaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGaa                                                          <  1:295361/64‑1 (MQ=255)

                  aaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGaa                                                          <  1:2978588/64‑1 (MQ=255)

                  aaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGaa                                                          <  1:842820/64‑1 (MQ=255)

                  aaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGaa                                                          <  1:2478178/64‑1 (MQ=255)

                  aaTATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATg                                                   <  1:3651865/71‑1 (MQ=255)

                    tataAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGaca                                                                       >  1:440131/1‑49 (MQ=255)

                     ataAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAg                                                 >  1:1465392/1‑70 (MQ=255)

                     ataAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAg                                                 >  1:486916/1‑70 (MQ=255)

                      taAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGca                                               <  1:3369688/71‑1 (MQ=255)

                        aaaaTATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGca                                               >  1:182441/1‑69 (MQ=255)

                          aaTATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGa                                           <  1:3483135/71‑1 (MQ=255)

                          aaTATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGa                                           <  1:1130121/71‑1 (MQ=255)

                            tatCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAatat                                                       <  1:3286244/57‑1 (MQ=255)

                            tatCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAatat                                                       <  1:2520817/57‑1 (MQ=255)

                            tatCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAatat                                                       <  1:1060766/57‑1 (MQ=255)

                              tCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACTGAGGaa                                                          <  1:2933/52‑1 (MQ=255)

                              tCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGaa                                                          <  1:3558472/52‑1 (MQ=255)

                              tCAATGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAAc                                        >  1:233607/1‑70 (MQ=255)

                              tCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAAtatta                                                     >  1:45522/1‑57 (MQ=255)

                              tCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAAtatta                                                     >  1:562938/1‑57 (MQ=255)

                              tCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAAc                                        >  1:1295629/1‑70 (MQ=255)

                                aaTGAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAAt                                     >  1:251242/1‑71 (MQ=255)

                                aaTGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAAt                                     >  1:1399545/1‑71 (MQ=255)

                                  tGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAAtt                                    >  1:310612/1‑70 (MQ=255)

                                   gAGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAatat                                                       <  1:30177/50‑1 (MQ=255)

                                    aGTCAATCAATAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGaa                                 <  1:880900/71‑1 (MQ=255)

                                    aGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGaa                                 <  1:2803770/71‑1 (MQ=255)

                                    aGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGaa                                 <  1:1427873/71‑1 (MQ=255)

                                      tcaatcaaTAATAATTTGGCATCACGAGACACATCACAGAGGAatat                                                       <  1:1805515/47‑1 (MQ=255)

                                        aatcaatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAatat                             >  1:2132943/1‑71 (MQ=255)

                                        aatcaatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAatat                             >  1:520303/1‑71 (MQ=255)

                                        aatcaatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAatat                             >  1:2524686/1‑71 (MQ=255)

                                        aatcaatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAata                              >  1:2487842/1‑70 (MQ=255)

                                          tcaatAATAATTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGa                                  <  1:2831485/64‑1 (MQ=255)

                                          tcaatAATAATTTGGCATCACGAGACACATCACAGAGGaa                                                          <  1:2039625/40‑1 (MQ=255)

                                          tcaatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTc                           <  1:2069132/71‑1 (MQ=255)

                                          tcaatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTc                           <  1:1095058/71‑1 (MQ=255)

                                           caatAATAATTTGGCATCACGAGACACATCACAGAGGa                                                           >  1:278774/1‑38 (MQ=255)

                                           caatAATAATTTGGCATCACGAGACACATCACAGAGGa                                                           >  1:1482478/1‑38 (MQ=255)

                                           caatAATAATTTGGCATCACGAGACACATCACAGAGGa                                                           >  1:2972545/1‑38 (MQ=255)

                                           caatAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTc                           >  1:3279786/1‑70 (MQ=255)

                                            aataataatTTGGCATCACGAGACGCATCACAGAGGAAtatta                                                     >  1:1924896/1‑43 (MQ=255)

                                            aataataatTTGGCATCACGAGACACATCACAGAGGAata                                                        >  1:2535991/1‑40 (MQ=255)

                                            aataataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACaa                                      >  1:2695792/1‑58 (MQ=255)

                                            aataataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaa                         >  1:4007645/1‑71 (MQ=255)

                                            aataataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaa                         >  1:3107017/1‑71 (MQ=255)

                                            aataataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaa                         >  1:3709864/1‑71 (MQ=255)

                                            aataataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaa                         >  1:127260/1‑71 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATg                                                   <  1:3069199/43‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATg                                                   <  1:2335489/43‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATg                                                   <  1:3089645/43‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATg                                                   <  1:713164/43‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:1940966/62‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:3532512/62‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:2169601/62‑1 (MQ=255)

                                              taataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:1964211/62‑1 (MQ=255)

                                               aataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaataa                      >  1:1626740/1‑71 (MQ=255)

                                                ataatTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaataa                      >  1:1341695/1‑70 (MQ=255)

                                                ataatTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaataa                      >  1:1107079/1‑70 (MQ=255)

                                                ataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAg                                                 >  1:2778721/1‑43 (MQ=255)

                                                ataatTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCaataa                      <  1:2115436/70‑1 (MQ=255)

                                                 taatTTGGCATCACGAGACACATCACAGAGGAATATTCTGAGCACAGAAACAATTGAAATATTc                           <  1:865206/64‑1 (MQ=255)

                                                  aatTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAg                   >  1:2667595/1‑71 (MQ=255)

                                                  aatTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAg                   >  1:506077/1‑71 (MQ=255)

                                                   atTTGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAg                   >  1:3001378/1‑70 (MQ=255)

                                                    tttGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:1490207/56‑1 (MQ=255)

                                                    tttGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:1329408/56‑1 (MQ=255)

                                                    tttGGCATCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGaaa                                <  1:3918614/56‑1 (MQ=255)

                                                        gCATCAGGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGtgatg              <  1:2596427/70‑1 (MQ=255)

                                                        gCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGtgatg              <  1:1985080/70‑1 (MQ=255)

                                                        gCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGtgatg              <  1:29170/70‑1 (MQ=255)

                                                        gCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGtgatg              <  1:3378639/70‑1 (MQ=255)

                                                           tCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAAt                                     <  1:3602492/44‑1 (MQ=255)

                                                           tCACGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTTATGAATg          <  1:752963/71‑1 (MQ=255)

                                                            cACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAata                              >  1:3267254/1‑50 (MQ=255)

                                                             aCGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATggg        >  1:774134/1‑71 (MQ=255)

                                                             aCGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATggg        >  1:470130/1‑71 (MQ=255)

                                                             aCGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATggg        >  1:2096181/1‑71 (MQ=255)

                                                             aCGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATggg        >  1:2351245/1‑71 (MQ=255)

                                                             aCGAGACGCATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATggg        >  1:2540527/1‑71 (MQ=255)

                                                             aCGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGaa            >  1:2976815/1‑67 (MQ=255)

                                                               gagaCACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCa      <  1:37903/71‑1 (MQ=255)

                                                               gagaCACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCa      <  1:2673847/71‑1 (MQ=255)

                                                                agaCACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCa      >  1:1995745/1‑70 (MQ=255)

                                                                agaCACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCa      >  1:2346743/1‑70 (MQ=255)

                                                                  acacATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGt                  <  1:3470652/56‑1 (MQ=255)

                                                                  acacATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGt                  <  1:2977771/56‑1 (MQ=255)

                                                                   cacaTCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCAAATc  <  1:1088807/71‑1 (MQ=255)

CATAATTTAAAAAAGATAAATATAAAAATATCAATGAGTCAATCAATAATAATTTGGCATCACGAGACACATCACAGAGGAATATTATGAGCACAGAAACAATTGAAATATTCAATAATAGTGATGAATGGGCAAATC  >  W3110S.gb/2989838‑2989975

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