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	2,572,941	G→A	84.6%	intergenic (+1709/‑70)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,572,941	0	G	A	84.6%	176.9 / 22.9	78	intergenic (+1709/‑70)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (5/7); new base A (34/32); total (39/39)
Fisher's exact test for biased strand distribution p-value = 7.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

AAATCATTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGT  >  minE/2572875‑2573004

aaaTCATTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTc                                                             >  1:1169768/1‑71 (MQ=255)

aaaTCATTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTc                                                             >  1:5595745/1‑71 (MQ=255)

aaaTCATTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTc                                                             >  1:3026132/1‑71 (MQ=255)

aaaTCATTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTc                                                             >  1:3004214/1‑71 (MQ=255)

     aTTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTaa                                                         <  1:272107/70‑1 (MQ=255)

       ttggttggCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGa                                                       >  1:4969468/1‑70 (MQ=255)

        tggttggCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGata                                                     >  1:1920790/1‑71 (MQ=255)

         ggttggCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGata                                                     <  1:3030054/70‑1 (MQ=255)

           ttggCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGt                                                           <  1:1525345/62‑1 (MQ=255)

              gcgcACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGc                                                <  1:785101/70‑1 (MQ=255)

                    tGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGa                                                       <  1:5088121/57‑1 (MQ=255)

                     ggAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGc                                                <  1:3418652/63‑1 (MQ=255)

                      gAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCg                                                            >  1:3158720/1‑50 (MQ=255)

                      gAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCa                                                  >  1:5616688/1‑60 (MQ=255)

                      gAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:1312736/65‑1 (MQ=255)

                      gAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATAcc                                       >  1:125108/1‑71 (MQ=255)

                        ataatCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGa                                     >  1:4278370/1‑71 (MQ=255)

                           atCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGata                                   >  1:3104097/1‑70 (MQ=255)

                             cTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGTaa                                                         >  1:1915268/1‑46 (MQ=255)

                             cTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGTaa                                                         >  1:5615037/1‑46 (MQ=255)

                             cTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGTa                                                          >  1:1512673/1‑45 (MQ=255)

                              tGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGa                                                       <  1:3625875/47‑1 (MQ=255)

                              tGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGa                                                       <  1:1995288/47‑1 (MQ=255)

                                 gTTTTATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATataaataa                            <  1:1251632/71‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTc                                                             >  1:377836/1‑35 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTa                                                          <  1:1831357/38‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTa                                                          <  1:4704160/38‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGat                                                      <  1:2575576/42‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGat                                                      <  1:3343784/42‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGat                                                      <  1:590753/42‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGat                                                      <  1:2392739/42‑1 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGa                                                       >  1:2717102/1‑41 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGa                                                       >  1:4850804/1‑41 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAaataat                           >  1:5455667/1‑69 (MQ=255)

                                    ttATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAaataat                           >  1:1583118/1‑69 (MQ=255)

                                     tATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGat                                                      <  1:2713864/41‑1 (MQ=255)

                                     tATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:3780635/50‑1 (MQ=255)

                                     tATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:2642622/50‑1 (MQ=255)

                                     tATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAaataat                           >  1:2388573/1‑68 (MQ=255)

                                     tATCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAAtaataa                         <  1:4101268/70‑1 (MQ=255)

                                      aTCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGatat                                                    >  1:205479/1‑42 (MQ=255)

                                      aTCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCa                                              >  1:5560245/1‑48 (MQ=255)

                                      aTCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATataaata                             >  1:813629/1‑65 (MQ=255)

                                      aTCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATataaata                             >  1:983441/1‑65 (MQ=255)

                                       tCACTACAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGAc                      >  1:2666502/1‑71 (MQ=255)

                                       tCACTACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGa                       <  1:4541958/70‑1 (MQ=255)

                                           tACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:3849703/44‑1 (MQ=255)

                                           tACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:5276767/44‑1 (MQ=255)

                                           tACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:4474490/44‑1 (MQ=255)

                                           tACAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCAc                                             <  1:4783862/44‑1 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAc                  <  1:3300573/69‑1 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAc                  <  1:2417444/69‑1 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAc                  <  1:1254247/69‑1 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACt                 <  1:1609978/70‑1 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACta                                           >  1:3514225/1‑44 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGa                                     >  1:2080281/1‑50 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGa                                     >  1:1074891/1‑50 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGa                       >  1:2362670/1‑64 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAcc                 <  1:4655347/70‑2 (MQ=255)

                                             cAGCTTATAGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAc                  <  1:5263584/69‑1 (MQ=255)

                                                cTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATAcc                                       <  1:5386661/45‑1 (MQ=255)

                                                  tataGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAcc                 <  1:2420840/65‑2 (MQ=255)

                                                  tataGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCAc                  >  1:2460938/1‑64 (MQ=255)

                                                   ataGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATataa                                <  1:5412653/49‑1 (MQ=255)

                                                    taGAGGCTTAAGGAAATTCGTAAGATATCAGCCACtata                                         >  1:5275196/1‑39 (MQ=255)

                                                    taGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTg               >  1:4046264/1‑65 (MQ=255)

                                                     agagGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAAc          >  1:2902988/1‑69 (MQ=255)

                                                         gCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACg    >  1:1505926/1‑71 (MQ=255)

                                                          cTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACgg   <  1:557743/71‑1 (MQ=255)

                                                           ttAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACt                     >  1:1551219/1‑52 (MQ=255)

                                                             aaGGAAATTCGTAAGATATCAGCCACTATACCGATataaa                               >  1:4351217/1‑40 (MQ=255)

                                                             aaGGAAATTCGTAAGATATCAGCCACTATACCGATataaa                               >  1:2532043/1‑40 (MQ=255)

                                                             aaGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGa                       >  1:2256599/1‑48 (MQ=255)

                                                             aaGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGa                       >  1:2112574/1‑48 (MQ=255)

                                                             aaGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGt  <  1:376872/69‑1 (MQ=255)

                                                              aGGAAATTCGTAAGATATCAGCCACTATACCGATATAAAtaataa                         <  1:5513069/45‑1 (MQ=255)

                                                              aGGAAATTCGTAAGATATCAGCCACTATACCGATATAAAtaataa                         <  1:584880/45‑1 (MQ=255)

                                                               ggAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTc                    <  1:2601689/49‑1 (MQ=255)

AAATCATTTGGTTGGCGCACTGGAATAATCTGAGTTTTATCACTACAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGT  >  minE/2572875‑2573004

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