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	1,804,377	A→G	21.0%	intergenic (‑93/‑431)	thrS ← / → arpB	threonyl‑tRNA synthetase/ECK1718:JW5278:b1720; hypothetical protein, N‑ter fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,804,377	0	A	G	21.0%	167.4 / 42.4	81	intergenic (‑93/‑431)	thrS/arpB	threonyl‑tRNA synthetase/ECK1718:JW5278:b1720; hypothetical protein, N‑ter fragment
Reads supporting (aligned to +/- strand): ref base A (34/30); new base G (8/9); total (42/39)
Fisher's exact test for biased strand distribution p-value = 7.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

CCCACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTC  >  W3110S.gb/1804310‑1804438

cccACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:2803868/71‑1 (MQ=255)

cccACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:1470092/71‑1 (MQ=255)

  cacaCGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACaaa                                                          >  1:3458070/1‑71 (MQ=255)

  cacaCGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACaaa                                                          >  1:2333900/1‑71 (MQ=255)

    cacGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATg                                                        >  1:1088585/1‑71 (MQ=255)

    cacGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATg                                                        >  1:2632215/1‑71 (MQ=255)

    cacGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATg                                                        >  1:1344903/1‑71 (MQ=255)

        aaaGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTaa                                                    <  1:3138435/71‑1 (MQ=255)

         aaGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:1819520/62‑1 (MQ=255)

         aaGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:3710491/62‑1 (MQ=255)

         aaGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:2582096/62‑1 (MQ=255)

         aaGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:2577492/62‑1 (MQ=255)

          aGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcaaca                                                            <  1:1095777/61‑1 (MQ=255)

          aGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAAt                                                  >  1:3934002/1‑71 (MQ=255)

              cacaTACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGt                                              >  1:818130/1‑71 (MQ=255)

                 aTACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCcgaca                                                            <  1:3871779/54‑1 (MQ=255)

                  tACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCg                                           >  1:1816918/1‑70 (MQ=255)

                   aCAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCg                                           >  1:1627408/1‑69 (MQ=255)

                   aCAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGc                                          >  1:732550/1‑70 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTaaa                                                   >  1:1274593/1‑60 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTaaa                                                   >  1:1042811/1‑60 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTaaa                                                   >  1:1078705/1‑60 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:2302709/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:26633/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:3835843/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:3588677/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:1675484/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:3846983/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:3900671/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:3920844/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:447532/1‑71 (MQ=255)

                    cAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCaa                                        >  1:980051/1‑71 (MQ=255)

                        gAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAg                                    >  1:2753241/1‑71 (MQ=255)

                              tttGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTacac                              <  1:3964340/71‑1 (MQ=255)

                                tGTTTATTAACAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTAcaca                             <  1:2413985/70‑1 (MQ=255)

                                     attaACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGCTACACAAATGa                        <  1:635363/70‑1 (MQ=255)

                                        aaCAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAg                     <  1:3345014/70‑1 (MQ=255)

                                        aaCAGTTCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAg                     <  1:2066154/70‑1 (MQ=255)

                                        aaCAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa                    >  1:2563460/1‑71 (MQ=255)

                                        aaCAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa                    >  1:811437/1‑71 (MQ=255)

                                         aCAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa                    <  1:321880/70‑1 (MQ=255)

                                           aGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa                      <  1:3806352/66‑1 (MQ=255)

                                            gTTCATTGCGAAACCATCTAGGCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:3246317/71‑1 (MQ=255)

                                            gTTCATTGCGAAACCATCTAGCCAACAAATGCTaa                                                    <  1:1764896/35‑1 (MQ=255)

                                            gTTCATTGCGAAACCATCTAGCCAACAAATGCTaa                                                    <  1:2750987/35‑1 (MQ=255)

                                            gTTCATTGCGAAACCATCTAGCCAACAAATGCTaa                                                    <  1:3882599/35‑1 (MQ=255)

                                             ttCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATg                         <  1:2145094/61‑1 (MQ=255)

                                             ttCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTa               <  1:155444/71‑1 (MQ=255)

                                             ttCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTa               <  1:950087/71‑1 (MQ=255)

                                             ttCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTa               <  1:38225/71‑1 (MQ=255)

                                             ttCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTa               <  1:1709006/71‑1 (MQ=255)

                                             ttCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTa               <  1:3730440/71‑1 (MQ=255)

                                              tCATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGtt                                             >  1:119456/1‑40 (MQ=255)

                                               cATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACaaa                           >  1:1266385/1‑57 (MQ=255)

                                               cATTGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACaaa                           >  1:3664725/1‑57 (MQ=255)

                                               cATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc             >  1:587632/1‑71 (MQ=255)

                                               cATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc             >  1:1148066/1‑71 (MQ=255)

                                               cATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc             >  1:2375436/1‑71 (MQ=255)

                                               cATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc             >  1:130934/1‑71 (MQ=255)

                                               cATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc             >  1:2324922/1‑71 (MQ=255)

                                                aTTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAAc             <  1:386130/70‑1 (MQ=255)

                                                  tgggAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctc          >  1:3269884/4‑71 (MQ=255)

                                                  tGCGAAACCATCTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGa                        >  1:2348934/1‑57 (MQ=255)

                                                    cGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctct         <  1:2776095/70‑1 (MQ=255)

                                                    cGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCtctc        <  1:93215/71‑1 (MQ=255)

                                                        aCCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCt    <  1:2800911/71‑1 (MQ=255)

                                                         ccATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa                      <  1:1758008/52‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:2795593/55‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:1447891/55‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:1359974/55‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:1748927/55‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:2573836/55‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctct         <  1:2403612/62‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctct         <  1:627849/62‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctct         <  1:3020833/62‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctct         <  1:2727383/62‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACctc          <  1:3011263/61‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTc  <  1:1228512/69‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTc  <  1:260013/69‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTc  <  1:2000915/69‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGAACACAAATGAAAGa                    <  1:702191/51‑1 (MQ=255)

                                                            tCTAGCCAACAAATGCTAAATTGGTGCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTc  <  1:2879711/69‑1 (MQ=255)

                                                             cTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa                    >  1:1046687/1‑50 (MQ=255)

                                                             cTAGCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa                    >  1:3904794/1‑50 (MQ=255)

                                                             cTAGCAGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGa                    >  1:3900804/1‑50 (MQ=255)

                                                                gCCGACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACAtt                <  1:615662/51‑1 (MQ=255)

                                                                gCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa                      >  1:684614/1‑45 (MQ=255)

                                                                gCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa                      >  1:3967884/1‑45 (MQ=255)

                                                                gCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGaaa                      >  1:1346000/1‑45 (MQ=255)

CCCACACGAAAGATCACATACAAAGAAAAATTTGTTTATTAACAGTTCATTGCGAAACCATCTAGCCAACAAATGCTAAATTGGTTCGCAATCAGGTACACAAATGAAAGACATTAACCTCTCACCTTC  >  W3110S.gb/1804310‑1804438

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A