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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,841,727	C→T	54.8%	A126T (GCC→ACC)	hycH ←	protein required for maturation of hydrogenase 3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,841,727	0	C	T	54.8%	21.7 / 130.8	93	A126T (GCC→ACC)	hycH	protein required for maturation of hydrogenase 3
Reads supporting (aligned to +/- strand): ref base C (24/18); new base T (26/25); total (50/43)
Fisher's exact test for biased strand distribution p-value = 6.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCG  >  W3110S.gb/2841664‑2841789

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGtttt                                                           >  1:302179/1‑69 (MQ=255)

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGtttt                                                           >  1:532169/1‑69 (MQ=255)

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGtttt                                                           >  1:484952/1‑69 (MQ=255)

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGttt                                                            <  1:2757467/68‑1 (MQ=255)

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGttt                                                            <  1:3393703/68‑1 (MQ=255)

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGttt                                                            <  1:1484990/68‑1 (MQ=255)

catGCTATTGACAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGttt                                                            <  1:3489222/68‑1 (MQ=255)

   gCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                        <  1:2911162/69‑1 (MQ=255)

   gCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                        <  1:3527236/69‑1 (MQ=255)

   gCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                        <  1:1445119/69‑1 (MQ=255)

      aTTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgat                                                     <  1:2379742/69‑1 (MQ=255)

       ttGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    >  1:24397/1‑69 (MQ=255)

       ttGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    >  1:2962132/1‑69 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatga                                                   >  1:61079/1‑68 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGaa                                                  >  1:733340/1‑69 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGaa                                                  >  1:2509617/1‑69 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGaa                                                  >  1:347834/1‑69 (MQ=255)

          ccAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAat                                                 >  1:3273318/1‑69 (MQ=255)

            aaCACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAatat                                               >  1:2004509/1‑69 (MQ=255)

             acacAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAatat                                               <  1:142729/68‑1 (MQ=255)

             acacAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAatat                                               >  1:370076/1‑68 (MQ=255)

             acacAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATc                                              >  1:1983339/1‑69 (MQ=255)

              cacaGAGTAAAACGTCGGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCa                                             <  1:392372/69‑1 (MQ=255)

                caGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCa                                             >  1:3354281/1‑67 (MQ=255)

                caGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCa                                             >  1:792146/1‑67 (MQ=255)

                caGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCa                                             >  1:94543/1‑67 (MQ=255)

                caGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCa                                             >  1:2817283/1‑67 (MQ=255)

                 agagTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    <  1:1078368/59‑1 (MQ=255)

                 agagTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    <  1:1861285/59‑1 (MQ=255)

                 agagTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    <  1:1056384/59‑1 (MQ=255)

                 agagTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    <  1:694695/59‑1 (MQ=255)

                 agagTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                    <  1:2429563/59‑1 (MQ=255)

                     tAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGaa                                                  >  1:788155/1‑57 (MQ=255)

                     tAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATgcagca                                      >  1:2964859/1‑69 (MQ=255)

                     tAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATgcagca                                      >  1:2800242/1‑69 (MQ=255)

                     tAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATgcagca                                      >  1:1946989/1‑69 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATa                                    <  1:2984685/69‑1 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATa                                    <  1:3647688/69‑1 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATa                                    <  1:1897275/69‑1 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATa                                    >  1:1769044/1‑69 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATa                                    >  1:1213090/1‑69 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgatg                                                    >  1:1436783/1‑53 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgatg                                                    >  1:1357894/1‑53 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgatg                                                    >  1:3705723/1‑53 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgatg                                                    >  1:3556882/1‑53 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgatg                                                    >  1:2581043/1‑53 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtgatg                                                    >  1:2321150/1‑53 (MQ=255)

                       aaaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATa                                    >  1:3703410/1‑69 (MQ=255)

                          cGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                 <  1:1956585/69‑1 (MQ=255)

                           gtcagtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTa                                <  1:1711796/69‑1 (MQ=255)

                           gtcagtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTa                                <  1:2571875/69‑1 (MQ=255)

                                 caCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATc                                              >  1:3132183/1‑49 (MQ=255)

                                    gCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                       <  1:1324915/69‑1 (MQ=255)

                                    gCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                       <  1:119729/69‑1 (MQ=255)

                                    gCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                       <  1:1155998/69‑1 (MQ=255)

                                         ctcctcACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 >  1:2557674/1‑54 (MQ=255)

                                         ctcctcACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                  <  1:2997945/69‑1 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                       >  1:1662857/1‑63 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTcc                 >  1:2509828/1‑69 (MQ=255)

                                              cACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCAt               <  1:2020955/67‑1 (MQ=255)

                                              cACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 <  1:1291234/49‑1 (MQ=255)

                                              cACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 <  1:2820140/49‑1 (MQ=255)

                                              cACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 <  1:1067815/49‑1 (MQ=255)

                                               aCCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                       <  1:205083/58‑1 (MQ=255)

                                               aCCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTcc            >  1:3139184/1‑69 (MQ=255)

                                               aCCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTcc            >  1:2600807/1‑69 (MQ=255)

                                                 cATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTcc            <  1:1258154/67‑1 (MQ=255)

                                                 cATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCct           <  1:3624725/68‑1 (MQ=255)

                                                  aTCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgc         >  1:391374/1‑69 (MQ=255)

                                                  aTCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgc         >  1:499281/1‑69 (MQ=255)

                                                  aTCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgc         >  1:3606929/1‑69 (MQ=255)

                                                    cAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgctg       >  1:749013/1‑69 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                            <  1:2332701/47‑1 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                            <  1:3621838/47‑1 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                            <  1:226033/47‑1 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTGctgctg       >  1:827460/1‑68 (MQ=255)

                                                     aaaTAGATGGCGTTTTCCTGATGAATATCATgcag                                        <  1:317888/35‑1 (MQ=255)

                                                     aaaTAGATGGCGTTTTCCTGATGAATATCATgcag                                        <  1:1352372/35‑1 (MQ=255)

                                                     aaaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 >  1:2028607/1‑42 (MQ=255)

                                                     aaaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 >  1:3691091/1‑42 (MQ=255)

                                                     aaaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 >  1:2232280/1‑42 (MQ=255)

                                                        tAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgctgctg    >  1:826741/1‑68 (MQ=255)

                                                        tAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgctgct     >  1:2288343/1‑67 (MQ=255)

                                                         aGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                            >  1:3712357/1‑43 (MQ=255)

                                                         aGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                            >  1:2355576/1‑43 (MQ=255)

                                                         aGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCg  <  1:3175783/69‑1 (MQ=255)

                                                         aGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCg  <  1:3138346/69‑1 (MQ=255)

                                                         aGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCg  <  1:450383/69‑1 (MQ=255)

                                                         aGATGGTGTTTTCCTGATGAATATCATGCAGCATAATTAACAg                            >  1:283079/1‑43 (MQ=38)

                                                          gATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 <  1:1052429/37‑1 (MQ=255)

                                                          gATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                 <  1:2188848/37‑1 (MQ=255)

                                                           aTGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCg  <  1:2479261/67‑1 (MQ=255)

                                                             ggCGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                            >  1:973496/1‑39 (MQ=255)

CATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCG  >  W3110S.gb/2841664‑2841789

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