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	2,572,989	T→C	68.2%	intergenic (+1757/‑22)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,572,989	0	T	C	68.2%	102.0 / 66.3	85	intergenic (+1757/‑22)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (11/16); new base C (30/28); total (41/44)
Fisher's exact test for biased strand distribution p-value = 3.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01

CAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCT  >  minE/2572920‑2573054

cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACt                                                                   <  1:1609978/70‑1 (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)

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

                    aaaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAAttt                                               >  1:2583266/3‑70 (MQ=255)

                     aaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:4890884/2‑60 (MQ=255)

                       ttCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAAc                                                            <  1:1149863/54‑1 (MQ=255)

                       ttCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAAc                                                            <  1:4385793/54‑1 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCa                                                               >  1:5093112/1‑50 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:1861708/1‑57 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:5285354/1‑57 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:3480274/1‑57 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:4183371/1‑57 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatga                                          >  1:3635096/1‑71 (MQ=255)

                          gTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatg                                        <  1:1468411/71‑1 (MQ=255)

                            aaGATATCAGCCACTATACCGATATAAATAATAAGACTCACCAGCAAACCAGa                                                        >  1:1989569/1‑53 (MQ=255)

                             aGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAatgatgat                                      >  1:2214150/1‑70 (MQ=255)

                             aGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatgat                                      >  1:2482950/1‑70 (MQ=255)

                             aGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatgat                                      >  1:2907180/1‑70 (MQ=255)

                             aGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatgat                                      >  1:1767164/1‑70 (MQ=255)

                             aGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatgat                                      >  1:2161061/1‑70 (MQ=255)

                              gATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatgatg                                     >  1:4478683/1‑70 (MQ=255)

                                 atCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAGACCAGACGGTAATTTAatgat                                         <  1:4458711/63‑1 (MQ=255)

                                 atCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgat                                         <  1:5314247/63‑1 (MQ=255)

                                 atCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAAc                                  >  1:2531556/1‑70 (MQ=255)

                                 atCAGCAACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACg                                 >  1:737234/1‑71 (MQ=255)

                                  tCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAAttt                                               <  1:91142/56‑1 (MQ=255)

                                    aGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGctt                              >  1:426772/1‑71 (MQ=255)

                                      ccACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTa                                              <  1:473413/53‑1 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:4655954/1‑41 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACCTGCAAACCAGa                                                        >  1:4856756/1‑41 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAat                                            >  1:3486863/1‑53 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGctttctt                          <  1:5555129/71‑1 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGctttctt                          <  1:4489296/71‑1 (MQ=255)

                                        aCTATACAGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATATAat                                            >  1:4807878/1‑53 (MQ=255)

                                          tataCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAat                                            <  1:4748805/51‑1 (MQ=255)

                                            taCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCtttctttc                        <  1:762442/69‑1 (MQ=255)

                                            taCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCtttctttc                        <  1:3234278/69‑1 (MQ=255)

                                             aCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                     >  1:1580362/1‑71 (MQ=255)

                                              ccGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                     >  1:829384/1‑70 (MQ=255)

                                                   ataaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCa                   <  1:334936/67‑1 (MQ=255)

                                                   ataaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCa                   <  1:2380240/67‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTa                                              <  1:1951560/39‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTa                                              <  1:1917131/39‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAatgatgatg                                     >  1:1594380/1‑48 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAatgatg                                        <  1:1172864/45‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAatgatg                                        <  1:3841072/45‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAatgatg                                        <  1:4181387/45‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAatgatg                                        <  1:5617347/45‑1 (MQ=255)

                                                      aataatAAGACTCACTTGCAAACCAGACGGTAATTTaa                                             >  1:926282/1‑38 (MQ=255)

                                                      aataatAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                    <  1:2714286/63‑1 (MQ=255)

                                                      aataatAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATgg               >  1:2412472/1‑68 (MQ=255)

                                                       ataataAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCt           <  1:5089875/71‑1 (MQ=255)

                                                         aataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAAt                 <  1:1121604/63‑1 (MQ=255)

                                                         aataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTa         >  1:4055548/1‑71 (MQ=255)

                                                          ataaGACTCACTTGCAAACCAGACGGTAATTTAatgatga                                       >  1:3519155/1‑40 (MQ=255)

                                                          ataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAAt                 <  1:4754504/62‑1 (MQ=255)

                                                          ataaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTAt        >  1:1491139/1‑71 (MQ=255)

                                                          ataaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTACGGCAATGGCGCTTa         <  1:3574053/70‑1 (MQ=255)

                                                           taaGACTCACCTGCAAACCAGACGGTAATTTAatgatgatg                                     <  1:2612306/41‑1 (MQ=255)

                                                            aaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGc                                <  1:1822302/45‑1 (MQ=255)

                                                            aaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGc                                <  1:3804695/45‑1 (MQ=255)

                                                            aaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGc                                <  1:3530424/45‑1 (MQ=255)

                                                             aGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGaa                                   >  1:5374641/1‑41 (MQ=255)

                                                             aGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATgg      <  1:3642069/70‑1 (MQ=255)

                                                              gACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCaa                  >  1:4435238/1‑57 (MQ=255)

                                                               aCTCACTTGCAAACCAGACGGTAATTTAATGATGATGaa                                   >  1:5255207/1‑39 (MQ=255)

                                                               aCTCACTTGCAAACCAGACGGTAATTTAATGATGATGaa                                   >  1:3995813/1‑39 (MQ=255)

                                                               aCTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttct                           <  1:376532/47‑1 (MQ=255)

                                                               aCTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttct                           <  1:451258/47‑1 (MQ=255)

                                                               aCTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttct                           <  1:330780/47‑1 (MQ=255)

                                                                cTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCt  <  1:3446117/71‑1 (MQ=255)

                                                                 tCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTATTTCCGGCAATGGCGCTTATGGTGc   <  1:421542/69‑1 (MQ=255)

                                                                 tCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATg       >  1:3748301/1‑65 (MQ=255)

                                                                  cACTTGCAAACCAGACGGTAATTTAATGATGATGAACGct                               <  1:4235039/40‑1 (MQ=255)

                                                                  cACTTGCAAACCAGACGGTAATTTAATGATGATGAACGct                               <  1:1895486/40‑1 (MQ=255)

                                                                  cACTTGCAAACCAGACGGTAATTTAATGATGATGAACGct                               <  1:290512/40‑1 (MQ=255)

                                                                   aCTTGCAAACCGGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTa         <  1:1610477/61‑1 (MQ=255)

                                                                   aCTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTa         <  1:5557695/61‑1 (MQ=255)

                                                                   aCTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGc   <  1:5644997/67‑1 (MQ=255)

                                                                    cTTGCAAACCAGACGGTAATTTAATGATGATGAACGcttt                             >  1:3236377/1‑40 (MQ=255)

                                                                    cTTGCAAACCAGACGGTAATTTAATGATGATGAACGcttt                             >  1:887016/1‑40 (MQ=255)

                                                                    cTTGCAAACCAGACGGTAATTTAATGATGATGAACGcttt                             >  1:5151102/1‑40 (MQ=255)

                                                                    cTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTg    <  1:4892274/65‑1 (MQ=255)

CAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCT  >  minE/2572920‑2573054

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