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 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,673,919	C→A	22.7%	G207C (GGT→TGT)	gntT ←	gluconate transporter, high‑affinity GNT I system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,673,919	0	C	A	22.7%	186.8 / 32.5	79	G207C (GGT→TGT)	gntT	gluconate transporter, high‑affinity GNT I system
Reads supporting (aligned to +/- strand): ref base C (30/31); new base A (12/6); total (42/37)
Fisher's exact test for biased strand distribution p-value = 2.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.93e-01

GAGAGGTCCAGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCGG  >  minE/2673850‑2673988

gagagGTCCAGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCt                                                                      >  1:949460/1‑71 (MQ=255)

       ccAGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGaa                                                               >  1:3169300/1‑71 (MQ=255)

        cAGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAAt                                                              <  1:2718459/71‑1 (MQ=255)

         aGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAAtt                                                             <  1:1040604/71‑1 (MQ=255)

         aGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAAtt                                                             <  1:2430961/71‑1 (MQ=255)

         aGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAAtt                                                             <  1:3931175/71‑1 (MQ=255)

          gACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTg                                                            >  1:2301252/1‑71 (MQ=255)

          gACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTg                                                            >  1:588030/1‑71 (MQ=255)

          gACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTg                                                            <  1:237913/71‑1 (MQ=255)

            cGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGc                                                          >  1:2394486/1‑71 (MQ=255)

                gACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGaa                                                               <  1:640423/62‑1 (MQ=255)

                 aCGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCt                                                         >  1:2982773/1‑67 (MQ=255)

                 aCGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATc                                                     >  1:886173/1‑71 (MQ=255)

                 aCGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATc                                                     >  1:519016/1‑71 (MQ=255)

                 aCGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATc                                                     <  1:2402020/71‑1 (MQ=255)

                   gCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGa                                                   >  1:1553719/1‑71 (MQ=255)

                    ccAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGAt                                                  <  1:1452475/71‑1 (MQ=255)

                     cAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATa                                                 >  1:3726731/1‑71 (MQ=255)

                      aaaGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATAc                                                >  1:2615375/1‑71 (MQ=255)

                        aGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCt                                              >  1:3778163/1‑71 (MQ=255)

                        aGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCt                                              >  1:3002204/1‑71 (MQ=255)

                           tCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATAc                                                <  1:713600/66‑1 (MQ=255)

                            cGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTc                                           >  1:174264/1‑70 (MQ=255)

                            cGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTg                                                            >  1:3243236/1‑53 (MQ=255)

                             ggCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCaa                                         >  1:3830473/1‑71 (MQ=255)

                             ggCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCTTTc                                           <  1:3598098/69‑1 (MQ=255)

                              gCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATAcc                                               <  1:382656/64‑1 (MQ=255)

                              gCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCtt                                             >  1:3604472/1‑66 (MQ=255)

                                aTCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAacac                                      <  1:2067347/71‑1 (MQ=255)

                                aTCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAaca                                       >  1:1488750/1‑70 (MQ=255)

                                 tctcTTCTTCGCTGAAGGTTTTCGGGCTGTAGAGACCt                                                                      <  1:1077829/38‑1 (MQ=255)

                                  ctctTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTcc                                                                   >  1:1871778/1‑40 (MQ=255)

                                   tcttctTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGaa                                                               >  1:158786/1‑43 (MQ=255)

                                   tcttctTCGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGaa                                                               >  1:691040/1‑43 (MQ=255)

                                    cttcttCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAac                                        <  1:2778028/65‑1 (MQ=255)

                                     ttcttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACAcgc                                    <  1:1390412/68‑1 (MQ=255)

                                     ttcttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAg                                 >  1:2560202/1‑71 (MQ=255)

                                     ttcttcGCTGAAGGTTTTCGCGCTGTAGAGACATTcc                                                                   >  1:147886/1‑37 (MQ=255)

                                     ttcttcGCTGAAGGTTTTCGCGCTGTAGAGACATTc                                                                    >  1:3666942/1‑36 (MQ=255)

                                     ttcttcGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAg                                 >  1:1717567/1‑71 (MQ=255)

                                     ttcttcGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAg                                 >  1:3947897/1‑71 (MQ=255)

                                       cttcGCTGAAGGTTTTCGCGCTGTAGAGATCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGa                                  <  1:956127/68‑1 (MQ=255)

                                       cttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATAcc                                               >  1:2824383/1‑55 (MQ=255)

                                       cttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGa                                  <  1:800900/68‑1 (MQ=255)

                                       cttcGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCg                               >  1:1582130/1‑71 (MQ=255)

                                        ttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGa                                                                <  1:3242546/37‑1 (MQ=255)

                                        ttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGa                                                                <  1:1071385/37‑1 (MQ=255)

                                        ttcGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGa                                                                <  1:1985031/37‑1 (MQ=255)

                                        ttcGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTa                                                       >  1:1567936/1‑46 (MQ=255)

                                        ttcGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTa                                                       >  1:3394083/1‑46 (MQ=255)

                                          cGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTa                             >  1:2214262/1‑70 (MQ=255)

                                          cGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTa                             <  1:1709633/70‑1 (MQ=255)

                                          cGCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGt                              <  1:3598677/69‑1 (MQ=255)

                                          cGCTGAAGGTTTACGCGCTGTAGAGACCTTCCGGAATTGGCt                                                         >  1:2356120/1‑42 (MQ=255)

                                           gCTGAAGGTTTTCGCGCTGTAGAGACATTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTaaa                           <  1:1483020/71‑1 (MQ=255)

                                               aaGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccgg                       <  1:1184811/71‑1 (MQ=255)

                                               aaGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccgg                       <  1:3622796/71‑1 (MQ=255)

                                               aaGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccg                        <  1:1256990/70‑1 (MQ=255)

                                                   ttttCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccggaccg                   >  1:1702798/1‑71 (MQ=255)

                                                   ttttCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccggaccg                   <  1:2910006/71‑1 (MQ=255)

                                                    tttCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGa                                                   >  1:2170510/1‑38 (MQ=255)

                                                     ttCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccggaccgg                  >  1:3714387/1‑70 (MQ=255)

                                                      tCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGc                 <  1:1349680/70‑1 (MQ=255)

                                                      tCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGc                 <  1:198360/70‑1 (MQ=255)

                                                      tCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGc                 <  1:869428/70‑1 (MQ=255)

                                                         cgcTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCgaga             <  1:3681465/71‑1 (MQ=255)

                                                         cgcTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCgaga             <  1:3042338/71‑1 (MQ=255)

                                                          gcTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTa                             >  1:413615/1‑54 (MQ=255)

                                                          gcTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGaa            <  1:989437/71‑1 (MQ=255)

                                                          gcTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGaa            >  1:178030/1‑71 (MQ=255)

                                                          gcTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGaa            <  1:2630798/71‑1 (MQ=255)

                                                            tGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAAt           >  1:3641594/1‑70 (MQ=255)

                                                              tAGAGACATTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATc          <  1:6605/69‑1 (MQ=255)

                                                                  gaCCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTc    <  1:2196042/71‑1 (MQ=255)

                                                                   aCCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAaccggacc                    >  1:877193/1‑54 (MQ=255)

                                                                   aCCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCg   >  1:473979/1‑71 (MQ=255)

                                                                   aCCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCg   >  1:392403/1‑71 (MQ=255)

                                                                   aCCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCg   <  1:1882776/71‑1 (MQ=255)

                                                                   aCCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCg   >  1:3605153/1‑71 (MQ=255)

                                                                    ccTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCgg  <  1:1014066/71‑1 (MQ=255)

GAGAGGTCCAGACGCTGACGCCAAAGCTCGGCATCTCTTCTTCGCTGAAGGTTTTCGCGCTGTAGAGACCTTCCGGAATTGGCTTATCGATACCTTTCAACACGCGAGCGTAAACCGGACCGGCGAGAATCACGGTCGG  >  minE/2673850‑2673988

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