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	2,572,989	T→C	34.7%	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	34.7%	46.0 / 43.5	49	intergenic (+1757/‑22)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (17/15); new base C (9/8); total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

CAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAGTGG  >  minE/2572920‑2573059

cAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACt                                                                        <  1:3208275/70‑1 (MQ=255)

  gCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACt                                                                        <  1:2518800/68‑1 (MQ=255)

      ataGGGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAc                                                                 >  1:2736402/1‑71 (MQ=255)

       taGAGGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAAcc                                                                <  1:925975/71‑1 (MQ=255)

         gagGCTTAAGGAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAg                                                              <  1:2379440/71‑1 (MQ=255)

             cTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACgg                                                          <  1:1317361/71‑1 (MQ=255)

                  ggAAATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAAtt                                                     >  1:1195105/1‑71 (MQ=255)

                    agaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTa                                                   <  1:1640416/71‑1 (MQ=255)

                     gaTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTaa                                                  <  1:985088/71‑1 (MQ=255)

                      aTTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAAttt                                                    <  1:330397/68‑1 (MQ=255)

                          gTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGa                                                             <  1:2304059/55‑1 (MQ=255)

                          gTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatgatg                                             <  1:3725785/71‑1 (MQ=255)

                           tAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTg                                                                      >  1:2644198/1‑45 (MQ=255)

                            aaGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAatgatgat                                           >  1:465486/1‑71 (MQ=255)

                                tatCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAAc                                                                 <  1:2021244/45‑1 (MQ=255)

                                    aGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctt                                   >  1:707130/1‑71 (MQ=255)

                                    aGCCACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGct                                    <  1:347885/70‑1 (MQ=255)

                                      ccACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttc                                 >  1:1027278/1‑71 (MQ=255)

                                       cACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttct                                <  1:204082/71‑1 (MQ=255)

                                       cACTATACCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGc                                     >  1:1499541/1‑66 (MQ=255)

                                         cTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTa                                                   <  1:3912471/50‑1 (MQ=255)

                                         cTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttcttt                              >  1:3545471/1‑71 (MQ=255)

                                          tataCCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGaa                                        <  1:3048141/60‑1 (MQ=255)

                                           ataCCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTcc                            >  1:3172466/1‑71 (MQ=255)

                                            taCCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTcc                            <  1:1457097/70‑1 (MQ=255)

                                            taCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCg                           >  1:2813101/1‑71 (MQ=255)

                                            taCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCg                           >  1:1536972/1‑71 (MQ=255)

                                             aCCGATATAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                          >  1:3672216/1‑71 (MQ=255)

                                              ccGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                          >  1:3292378/1‑70 (MQ=255)

                                              ccGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCgg                          >  1:144224/1‑70 (MQ=255)

                                               cGATATAAATAATAAGACTCCCTTGCAAACCAGACGGTAATTTAatgatgat                                           >  1:2235979/1‑52 (MQ=255)

                                               cGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAatgatgat                                           >  1:3805145/1‑52 (MQ=255)

                                               cGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGctttcttt                              >  1:3749088/1‑65 (MQ=255)

                                               cGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCggg                         >  1:430967/1‑69 (MQ=255)

                                                 atatAAATAATAAGACTCACCTGCAAACCAGACGGTAATTTAatg                                                >  1:3939717/1‑45 (MQ=255)

                                                  tataAATAATAAGACTCACTTGCAAACCAGACGGTa                                                        <  1:340704/36‑1 (MQ=255)

                                                   ataaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATgg                    >  1:3393344/1‑71 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACGAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATg                     <  1:2426717/69‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATg                     <  1:835341/69‑1 (MQ=255)

                                                    taaataaTAAGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATg                     <  1:2431339/69‑1 (MQ=255)

                                                      aataatAAGACTCACTTGCAAACCAGACGGTAATTTAatgatgatg                                          <  1:3351819/46‑1 (MQ=255)

                                                      aataatAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGc                         <  1:473085/63‑1 (MQ=255)

                                                          ataaGACTCACTTGCAAACCAGACGGTAATTTAatgatga                                            >  1:1845890/1‑40 (MQ=255)

                                                          ataaGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCtttctttc                             >  1:953257/1‑55 (MQ=255)

                                                          ataaGACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTAt             >  1:2996487/1‑71 (MQ=255)

                                                             aGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATgg           <  1:1051316/70‑1 (MQ=255)

                                                              gACTCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTa              <  1:1022296/66‑1 (MQ=255)

                                                                cTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGc        >  1:1913583/1‑70 (MQ=255)

                                                                 tCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGc        >  1:3257440/1‑69 (MQ=255)

                                                                 tCACCTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGc        >  1:1182209/1‑69 (MQ=255)

                                                                    cTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTa      <  1:2428203/68‑1 (MQ=255)

                                                                     ttGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAGTgg  >  1:3150937/1‑71 (MQ=255)

CAGCTTATAGAGGCTTAAGGAGATTCGTAAGATATCAGCCACTATACCGATATAAATAATAAGACTCACTTGCAAACCAGACGGTAATTTAATGATGATGAACGCTTTCTTTCCGGCAATGGCGCTTATGGTGCTAGTGG  >  minE/2572920‑2573059

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