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
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	834,950	T→G	20.0%	I1136M (ATT→ATG) ‡	narG →	nitrate reductase 1, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	834,950	0	T	G	20.0%	154.5 / 47.0	90	I1136M (ATT→ATG) ‡	narG	nitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand): ref base T (34/38); new base G (13/5); total (47/43)
Fisher's exact test for biased strand distribution p-value = 6.89e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

CGGTGGTCCGGTGGTCTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGA  >  minE/834881‑835017

cggtggtccggtggtcTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     <  1:121212/70‑1 (MQ=255)

cggtggtccggtggtcTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTg                                                                    <  1:3855379/71‑1 (MQ=255)

cggtggtccggtggtcTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTg                                                                    <  1:374314/71‑1 (MQ=255)

       ccggtggtcTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     >  1:4898462/1‑63 (MQ=255)

          attgtcTGGATCAGCGAAACAGATGCCCGAGAACTGACCATTGTCGATAACGACTGGGTGGAAGTATTCaa                                                          >  1:1820043/4‑71 (MQ=255)

            tgtcTGGATCAGCGAAACAGATGCCCGAGAACTGACCATTGTCGATAACGACTGGGTGGAAGTATTCAAcg                                                        >  1:2343164/2‑70 (MQ=255)

             gtcTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAg                                                       >  1:1649641/1‑71 (MQ=255)

             gtcTGGATCAGCGAAACAGATGCCCGAGAACTGACCATTGTCGATAACGACTGGGTGGAAGTATTCAAcgc                                                       >  1:899990/1‑69 (MQ=255)

              tcTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGc                                                      <  1:4850177/71‑1 (MQ=255)

              tcTGGATCAGCGAAACAGATGCCCGAGAACTGACCATTGTCGATAACGACTGGGTGGAAGTATTCAAcgc                                                       >  1:3427809/1‑68 (MQ=255)

                tGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCaa                                                    >  1:2835637/1‑71 (MQ=255)

                  gTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCaa                                                    <  1:948975/69‑1 (MQ=255)

                  gTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCaa                                                    <  1:3389306/69‑1 (MQ=255)

                   ttGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCaa                                                    <  1:3434384/68‑1 (MQ=255)

                     gAGTGAAGCCGATGCCAAAGATCTTGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTg                                               >  1:4234490/1‑71 (MQ=255)

                     gAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTg                                               >  1:4294503/1‑71 (MQ=255)

                     gAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTg                                               >  1:2770190/1‑71 (MQ=255)

                       gTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGct                                             <  1:3521631/71‑1 (MQ=255)

                        tGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGct                                             <  1:1526458/70‑1 (MQ=255)

                          aaGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           >  1:4154054/1‑70 (MQ=255)

                          aaGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           >  1:4765087/1‑70 (MQ=255)

                             ccGATGCCAAAGATCTGGTTATCGCCGATAACGACTGGATTGAAGt                                                                >  1:1898122/1‑46 (MQ=255)

                               gATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGaa                                                                  >  1:3142223/1‑42 (MQ=255)

                                 tGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTc                                                            <  1:207929/46‑1 (MQ=255)

                                 tGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTc                                                            <  1:2445789/46‑1 (MQ=255)

                                 tGCCAAAGATCTAGGTATCGCCGATAACGACTGGATTGAAGTCTTc                                                            <  1:5360145/46‑1 (MQ=255)

                                  gCCAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     <  1:1232104/36‑1 (MQ=255)

                                  gCCAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     <  1:5213061/36‑1 (MQ=255)

                                  gCCAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     <  1:4527175/36‑1 (MQ=255)

                                   ccAAAGATCTGGGTATCGCCGTTAACGACTGGATTGAAGTCTTCAACAGCAACGGTTCTCTGACTGCCCGt                                 <  1:618572/71‑1 (MQ=255)

                                   ccAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     <  1:2624745/35‑1 (MQ=255)

                                   ccAAAGATCTGGGTATCGCCGATAACGACTGGAtt                                                                     <  1:2038071/35‑1 (MQ=255)

                                   ccAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGt                                 >  1:2396364/1‑71 (MQ=255)

                                    cAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCa                                                     <  1:4976647/50‑1 (MQ=255)

                                    cAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGt                                 >  1:158524/1‑70 (MQ=255)

                                     aaaGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTc                                                            <  1:386399/42‑1 (MQ=255)

                                     aaaGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGc                               >  1:1479942/1‑71 (MQ=255)

                                       aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCaa                                                          >  1:875753/1‑42 (MQ=255)

                                       aGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCgg                             <  1:3748388/71‑1 (MQ=255)

                                       aGATCTGGGTATCGCCGA‑AACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGt                            >  1:133434/1‑71 (MQ=255)

                                        gATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTc                                                            >  1:1729848/1‑39 (MQ=255)

                                        gATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGt                            <  1:3713258/71‑1 (MQ=255)

                                         aTCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCaa                                                    <  1:815557/46‑1 (MQ=255)

                                           cTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTg                          >  1:1986201/1‑70 (MQ=255)

                                           cTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTg                          >  1:4659357/1‑70 (MQ=255)

                                           cTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTg                          >  1:1525425/1‑70 (MQ=255)

                                             gggTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCaa                                                    <  1:2345155/42‑1 (MQ=255)

                                             gggTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGt                         >  1:3106948/1‑69 (MQ=255)

                                              ggTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACgg                                                 >  1:64356/1‑44 (MQ=255)

                                              ggTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACgg                                                 >  1:834707/1‑44 (MQ=255)

                                               gTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagc                     <  1:4109995/71‑1 (MQ=255)

                                               gTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagc                     <  1:2836867/71‑1 (MQ=255)

                                                tATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGtt                           <  1:5235198/64‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCa                                                     <  1:3806446/36‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCa                                                     <  1:1963822/36‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCa                                                     <  1:5236720/36‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           <  1:2095486/46‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           <  1:5548519/46‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           <  1:5433227/46‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           <  1:4329922/46‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGctct                                           <  1:946040/46‑1 (MQ=255)

                                                  tCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTcagccag                  >  1:3045687/1‑71 (MQ=255)

                                                    gtcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACt                                       >  1:433713/3‑48 (MQ=12)

                                                    gtcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACt                                       >  1:3904438/3‑48 (MQ=12)

                                                    gtcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTca                       >  1:2057095/3‑64 (MQ=255)

                                                    gtcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACg                >  1:5386486/3‑71 (MQ=255)

                                                    gtcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACg                >  1:1991539/3‑71 (MQ=255)

                                                    gtcGATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACg                >  1:3982122/3‑71 (MQ=255)

                                                    gCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGGCAGCg                >  1:1210870/1‑71 (MQ=255)

                                                    gCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCg                >  1:4128563/1‑71 (MQ=255)

                                                    gCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCg                >  1:5591984/1‑71 (MQ=255)

                                                    gCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCg                >  1:1421242/1‑71 (MQ=255)

                                                       gATAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtg              <  1:3609679/70‑1 (MQ=255)

                                                        aTAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtgta            <  1:1640830/71‑2 (MQ=255)

                                                        aTAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGtt            >  1:1871631/1‑71 (MQ=255)

                                                         tAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtgtac           >  1:1578511/1‑69 (MQ=255)

                                                         tAACGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtgtac           >  1:25384/1‑69 (MQ=255)

                                                         tAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTc           <  1:4348712/71‑1 (MQ=255)

                                                          aaCGACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACGTGTAcc          >  1:5064802/1‑71 (MQ=255)

                                                          aaCGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTcc          >  1:4115595/1‑71 (MQ=255)

                                                          aaCGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTcc          >  1:4437493/1‑71 (MQ=255)

                                                             gACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtg              <  1:4463087/64‑1 (MQ=255)

                                                             gACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtg              <  1:4456176/64‑1 (MQ=255)

                                                             gACTGGGTGGAAGTATTCAACGCCAACGGCGCGCTGACTGCCCGCGCGGTGGTCAGCCAACgtg              <  1:2911574/64‑1 (MQ=255)

                                                             gACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGc       <  1:3507533/71‑1 (MQ=255)

                                                              aCTGGATTGAAGTCTTCAACAGAAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCa      <  1:4126060/71‑1 (MQ=255)

                                                               cTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAg     >  1:1206532/1‑71 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGt                         >  1:5522397/1‑48 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg    <  1:3770936/69‑1 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg    <  1:234117/69‑1 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg    <  1:4852113/69‑1 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg    <  1:3777645/69‑1 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg    <  1:4414455/69‑1 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAgg    <  1:1166388/69‑1 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGa  >  1:5364934/1‑71 (MQ=255)

                                                                  gATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGa  >  1:3396998/1‑71 (MQ=255)

                                                                   aTTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGt                            >  1:2849532/1‑44 (MQ=255)

CGGTGGTCCGGTGGTCTGGTTGAGTGAAGCCGATGCCAAAGATCTGGGTATCGCCGATAACGACTGGATTGAAGTCTTCAACAGCAACGGTGCTCTGACTGCCCGTGCGGTTGTCAGCCAGCGTGTTCCGGCAGGGA  >  minE/834881‑835017

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