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	1,763,636	A→G	31.4%	noncoding (208/1542 nt)	rrsG ←	16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,763,636	0	A	G	31.4%	59.1 / 36.1	51	noncoding (208/1542 nt)	rrsG	16S ribosomal RNA
Reads supporting (aligned to +/- strand): ref base A (19/16); new base G (14/2); total (33/18)
Fisher's exact test for biased strand distribution p-value = 2.81e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

GCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT  >  minE/1763567‑1763705

gCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGaa                                                                       <  1:1257934/70‑1 (MQ=255)

gCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAg                                                                      >  1:2916016/1‑71 (MQ=255)

   ttGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTc                                                                   >  1:2343296/1‑71 (MQ=255)

   ttGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTc                                                                   >  1:5547794/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:974628/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:2942877/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:5074764/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:119386/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:771191/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:925875/1‑71 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTcc                                                                  >  1:114823/1‑70 (MQ=255)

     ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATATGGGCACATCCGATGGCAAGAGGCCCGAAGGTccc                                                                 >  1:1696883/1‑71 (MQ=255)

         aGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGGACATCCGATGGCAAGAGGCCCGAAg                                                                      >  1:3210686/1‑62 (MQ=255)

         aGCCGTTACCCCACCAACAAGCTAATACCATCTGGGCACATCCGATGGCAAGAGGCCCGAAg                                                                      >  1:2690123/1‑62 (MQ=255)

          gCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCctct                                                            <  1:3569250/71‑1 (MQ=39)

           ccGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCctct                                                            <  1:2108670/70‑1 (MQ=255)

           ccGTTAACCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCtt                                                           >  1:4571/1‑71 (MQ=255)

             gTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGaa                                                                       >  1:4200871/1‑57 (MQ=255)

             gTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGaa                                                                       >  1:3338292/1‑57 (MQ=255)

             gTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTg                                                         >  1:1382268/1‑71 (MQ=39)

              ttACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTgg                                                        <  1:3372698/71‑1 (MQ=39)

                aCCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTc                                                      >  1:3126289/1‑71 (MQ=255)

                    catcaacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGc                                                  >  1:2447350/4‑71 (MQ=255)

                    caccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGc                                                  <  1:3180391/71‑1 (MQ=39)

                    caccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGc                                                  <  1:5381993/71‑1 (MQ=39)

                      ccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGa                                                >  1:995443/1‑71 (MQ=255)

                      ccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGGCTTGCGa                                                <  1:2204254/71‑1 (MQ=255)

                       caacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGa                                                <  1:1929766/70‑1 (MQ=39)

                        aacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGAcg                                              >  1:4273303/1‑70 (MQ=19)

                         acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGAcgt                                             <  1:2532711/71‑3 (MQ=9)

                         acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACAt                                             >  1:2293347/1‑71 (MQ=38)

                          caaGCTGATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGa                                                >  1:730146/1‑67 (MQ=255)

                          caaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAggg                                                                     >  1:3182716/1‑46 (MQ=255)

                          caaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACAt                                             >  1:1266945/1‑70 (MQ=37)

                           aaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTa                                           <  1:1685863/71‑1 (MQ=35)

                                    ccATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAt                                   >  1:1319619/1‑70 (MQ=35)

                                    ccATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAt                                   <  1:2495315/70‑1 (MQ=35)

                                    ccATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAt                                   >  1:2409465/1‑70 (MQ=35)

                                      aTCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTAt                                          <  1:1032279/61‑1 (MQ=35)

                                       tCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTa                                           <  1:2451853/59‑1 (MQ=35)

                                          gggCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTAt                                          <  1:3069787/57‑1 (MQ=35)

                                          gggCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAg                                <  1:3158037/67‑1 (MQ=35)

                                                   cGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCag                   >  1:5639759/1‑71 (MQ=34)

                                                   cGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCa                    <  1:282730/70‑1 (MQ=35)

                                                    gATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTAcc                           >  1:5042981/1‑62 (MQ=35)

                                                      tGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCg                                       >  1:963098/1‑48 (MQ=38)

                                                        gCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCagtagt               <  1:5492057/70‑1 (MQ=35)

                                                            gagGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATc           >  1:4754213/1‑70 (MQ=35)

                                                             agGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTcc                     <  1:1187490/59‑1 (MQ=35)

                                                             agGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATccc         >  1:273691/1‑71 (MQ=34)

                                                              ggCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCg                                       >  1:4986758/1‑40 (MQ=40)

                                                                cccGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCt      <  1:1067516/71‑1 (MQ=34)

                                                                 ccGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAtt                                  >  1:2341377/1‑42 (MQ=38)

                                                                   gAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCa   >  1:5403845/1‑71 (MQ=34)

                                                                   gAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCa   >  1:1593072/1‑71 (MQ=34)

                                                                    aaGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAtt                                  >  1:5234398/1‑39 (MQ=40)

                                                                    aaGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAtt                                  >  1:845373/1‑39 (MQ=40)

                                                                    aaGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTAtt                                  >  1:2930364/1‑39 (MQ=40)

                                                                    aaGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAt  >  1:1496276/1‑71 (MQ=34)

GCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT  >  minE/1763567‑1763705

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