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
A2 F8 I0 R2	296	77.6	4260404	88.1%	3753415	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,864,584	C→T	43.2%	A295A (GCC→GCT)	hflK →	modulator for HflB protease specific for phage lambda cII repressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,864,584	0	C	T	43.2%	24.3 / 73.1	58	A295A (GCC→GCT)	hflK	modulator for HflB protease specific for phage lambda cII repressor
Reads supporting (aligned to +/- strand): ref base C (18/14); new base T (12/13); total (31/27)
Fisher's exact test for biased strand distribution p-value = 5.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.96e-01

CCAACGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAGCCGCGC  >  minE/2864514‑2864654

ccAACGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGcc                                                                        >  1:2962320/1‑71 (MQ=255)

ccAACGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGcc                                                                        >  1:1303129/1‑71 (MQ=255)

  aaCGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCa                                                                      <  1:307991/71‑1 (MQ=255)

  aaCGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGAGTGCGTACAAGGCTCa                                                                      <  1:956800/71‑1 (MQ=255)

    cGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGCGGCGCGTGCGTACAAGGCCCa                                                                      >  1:893705/1‑69 (MQ=255)

    cGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGa                                                                    >  1:539393/1‑71 (MQ=255)

    cGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGa                                                                    >  1:3290154/1‑71 (MQ=255)

    cGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGa                                                                    >  1:3604256/1‑71 (MQ=255)

          tCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATc                                                               >  1:3079003/1‑70 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCa                                                                 >  1:4199174/1‑67 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATcc                                                              >  1:2660885/1‑70 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCt                                                             >  1:1223257/1‑71 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCt                                                             >  1:3069391/1‑71 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCt                                                             >  1:2524120/1‑71 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCt                                                             >  1:2402754/1‑71 (MQ=255)

           cAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCACAGACCATcc                                                              >  1:3889151/1‑70 (MQ=255)

             gCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTg                                                            >  1:1574345/1‑70 (MQ=255)

             gCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTg                                                            >  1:202904/1‑70 (MQ=255)

             gCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTg                                                            >  1:2173980/1‑70 (MQ=255)

                     cGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCa                                                    <  1:1609307/70‑1 (MQ=255)

                     cGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCa                                                    <  1:231814/70‑1 (MQ=255)

                         cGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTg                                               <  1:2655450/71‑1 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGAcc                                                                  >  1:4215676/1‑51 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTg                                               >  1:1070291/1‑70 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTg                                               >  1:1655546/1‑70 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGa                                              <  1:1057021/71‑1 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGa                                              <  1:473278/71‑1 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGa                                              <  1:1598328/71‑1 (MQ=255)

                          ggTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGa                                              <  1:258374/71‑1 (MQ=255)

                                gcgcAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGgc                                        >  1:198609/1‑71 (MQ=255)

                                     aCGTATCCTCGAAGAGGCGCTTGCGTACAAGGCTCAGACCATCCTgg                                                           <  1:2918080/47‑1 (MQ=255)

                                     aCGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTgg                                                           <  1:1674849/47‑1 (MQ=255)

                                     aCGTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTgg                                                           <  1:232101/47‑1 (MQ=255)

                                       gTATCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGaa                                                         >  1:2768083/1‑47 (MQ=255)

                                          tCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAggg                                                 >  1:2083846/1‑52 (MQ=255)

                                          tCCTCGAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAggg                                                 >  1:3747074/1‑52 (MQ=255)

                                            cTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTa                             >  1:629461/1‑70 (MQ=255)

                                              cGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTgg                                                           >  1:1746649/1‑38 (MQ=255)

                                               gAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGgcgc                                      >  1:1380049/1‑58 (MQ=255)

                                               gAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGTCGCGCTTTGCTaa                            <  1:4132862/68‑1 (MQ=255)

                                               gAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTaa                            <  1:317990/68‑1 (MQ=255)

                                               gAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAAc                          >  1:3405928/1‑70 (MQ=255)

                                               gAAGAGGCGCGTGCGTACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAAc                          >  1:812898/1‑70 (MQ=255)

                                                    ggCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAg                                            <  1:1563102/47‑1 (MQ=255)

                                                    ggCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAg                                            <  1:4227141/47‑1 (MQ=255)

                                                     gcgcGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGcc                   >  1:3232087/1‑71 (MQ=255)

                                                       gcgtgcgtACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCgg                 <  1:3415849/71‑1 (MQ=255)

                                                            cgtACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGaa                                             >  1:2721679/1‑38 (MQ=255)

                                                              tACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATaa          <  1:3131309/71‑1 (MQ=255)

                                                              tACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATaa          <  1:2935985/71‑1 (MQ=255)

                                                              tACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATaa          <  1:2924023/71‑1 (MQ=255)

                                                              tACAAGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATaa          <  1:2821036/71‑1 (MQ=255)

                                                                cAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAg        >  1:1420151/1‑71 (MQ=255)

                                                                cAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAg        >  1:4237597/1‑71 (MQ=255)

                                                                 aaGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTaa                            <  1:15956/50‑1 (MQ=255)

                                                                 aaGGCTCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTaa                            <  1:160281/50‑1 (MQ=255)

                                                                  aGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCgg                 <  1:3199334/60‑1 (MQ=255)

                                                                  aGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCgg                 <  1:3189391/60‑1 (MQ=255)

                                                                  aGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCgg                 <  1:2198765/60‑1 (MQ=255)

                                                                    gCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAGCcgc    <  1:1166423/71‑1 (MQ=255)

                                                                     cccAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAGCcgcg   <  1:1486054/71‑1 (MQ=255)

                                                                      ccAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAGCCgcgc  >  1:3181510/1‑71 (MQ=255)

CCAACGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAAGCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAGCCGCGC  >  minE/2864514‑2864654

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