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 R2	370	72.1	3738297	91.5%	3420541	62.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,572,989	T→C	7.5%	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	7.5%	149.7 / 3.4	53	intergenic (+1757/‑22)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (16/33); new base C (2/2); total (18/35)
Fisher's exact test for biased strand distribution p-value = 5.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAG  >  minE/2572920‑2573056

cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACtt                                                                    >  1:497022/1‑71 (MQ=255)

       taGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAc                                                              <  1:3280511/70‑1 (MQ=255)

        agagGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAc                                                              >  1:1297163/1‑69 (MQ=255)

           ggCTTAAGGAAATTCGTAAGATGTCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGAc                                                         >  1:3006214/1‑71 (MQ=255)

             cTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACgg                                                       <  1:2647293/71‑1 (MQ=255)

                   gagaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAAtt                                                  >  1:493408/1‑70 (MQ=255)

                   gagaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAAtt                                                  >  1:2010998/1‑70 (MQ=255)

                    agaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAc                                                              <  1:3300571/57‑1 (MQ=255)

                    agaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTa                                                <  1:3157943/71‑1 (MQ=255)

                     gaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGa                                                          <  1:3619598/60‑1 (MQ=255)

                     gaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGa                                                          <  1:2893990/60‑1 (MQ=255)

                        tCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAatga                                            >  1:2972118/1‑71 (MQ=255)

                          gTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAatgatg                                          <  1:619818/71‑1 (MQ=255)

                                 atCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAcc                                                             >  1:3292384/1‑45 (MQ=255)

                                   cAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAcc                                                             >  1:3438555/1‑43 (MQ=255)

                                    aGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGct                                 <  1:3494122/70‑1 (MQ=255)

                                    aGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGct                                 <  1:2876749/70‑1 (MQ=255)

                                    aGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGct                                 <  1:1330900/70‑1 (MQ=255)

                                     gCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGcttt                               <  1:3489300/71‑1 (MQ=255)

                                      ccACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttc                              >  1:2100725/1‑71 (MQ=255)

                                       cACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttct                             >  1:796904/1‑71 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttctt                            <  1:286569/71‑1 (MQ=255)

                                        aCTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttctt                            <  1:2493715/71‑1 (MQ=255)

                                          tataCCGATATAAATAATAAGACTCACTTGCAAACCa                                                            <  1:2606018/37‑1 (MQ=255)

                                          tataCCGATATAAACAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGctttcttt                           <  1:1235599/70‑1 (MQ=255)

                                            taCCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACg                                   <  1:2604146/60‑1 (MQ=255)

                                             aCCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                       >  1:3105408/1‑71 (MQ=255)

                                             aCCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                       >  1:855299/1‑71 (MQ=255)

                                              ccGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                       <  1:2597802/70‑1 (MQ=255)

                                              ccGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                      <  1:1770654/71‑1 (MQ=255)

                                               cGATATAAATAATAAGACTCACTTGCAAACCAGACGGTa                                                     >  1:23755/1‑39 (MQ=255)

                                                gATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCaa                    <  1:2366424/71‑1 (MQ=255)

                                                 atatAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAAt                   >  1:585878/1‑71 (MQ=255)

                                                 atatAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAAt                   >  1:1117127/1‑71 (MQ=255)

                                                    taaataaTAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                      <  1:1297051/65‑1 (MQ=255)

                                                    taaataaTAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                      <  1:2498539/65‑1 (MQ=255)

                                                    taaataaTAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATgg                 <  1:3401984/70‑1 (MQ=255)

                                                    taaataaTAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATgg                 <  1:2258209/70‑1 (MQ=255)

                                                      aataatAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttctt                            <  1:2322626/57‑1 (MQ=255)

                                                         aataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                      <  1:2806604/60‑1 (MQ=255)

                                                         aataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                      <  1:667705/60‑1 (MQ=255)

                                                          ataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTa           <  1:2540605/70‑1 (MQ=255)

                                                           taaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAAc                                    <  1:1331837/44‑1 (MQ=255)

                                                           taaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTa           <  1:2497575/69‑1 (MQ=255)

                                                           taaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATg         <  1:3523933/71‑1 (MQ=255)

                                                           taaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATg         <  1:3603025/71‑1 (MQ=255)

                                                           taaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATg         >  1:3577324/1‑71 (MQ=255)

                                                           taaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATg         >  1:2314387/1‑71 (MQ=255)

                                                              gACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTg      >  1:109426/1‑71 (MQ=255)

                                                                 tCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCt             <  1:2604881/61‑1 (MQ=255)

                                                                   aCTTGCAAACCAGACGGTAATTTAATGATGATGAACGctt                                >  1:3498164/1‑40 (MQ=255)

                                                                   aCTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAg  <  1:2251272/70‑1 (MQ=255)

                                                                   aCTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAg  <  1:1642018/70‑1 (MQ=255)

                                                                    cTTGCAAACCAGACGGTAATTTAATGATGATGAACGCtttctttc                          <  1:873274/45‑1 (MQ=255)

                                                                     ttGCAAACCAGACGGTAATTTAATGATGATGAACGctttcttt                           >  1:309388/1‑43 (MQ=255)

                                                                     ttGCAAACCAGACGGTAATTTAATGATGATGAACGctttcttt                           >  1:3310740/1‑43 (MQ=255)

                                                                     ttGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                      <  1:2611738/48‑1 (MQ=255)

CAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAG  >  minE/2572920‑2573056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A