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
A23 F67 I0 R1	35	27.8	1096780	91.1%	999166	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,708,718	G→A	25.2%	A600A (GCG→GCA)	rsxC →	SoxR [2Fe‑2S] reducing system protein RsxC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,708,718	0	G	A	25.2%	25.6 / 4.7	23	A600A (GCG→GCA)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
Reads supporting (aligned to +/- strand): ref base G (5/12); new base A (2/4); total (7/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

ATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAG  >  NC_000913/1708576‑1708859

aTCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgcg                                                                                                                                               >  1:4718/1‑143 (MQ=255)

 tCCACGTACAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgcgc                                                                                                                                              <  1:42491/143‑1 (MQ=255)

 tCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGCCGCAGCCGCTATTGCCCGTGCCAAAgcgc                                                                                                                                              >  1:468992/1‑143 (MQ=255)

    gcGTAAAACTGCCGCTGACGCAGCTATCGCCCGGGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCa                                                                                                                                           <  2:488043/142‑1 (MQ=11)

     cctAAACCTGCCCTTCAAGCAGCTCTCGCCCGCGCCAACGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCaa                                                                                                                                          <  1:136302/141‑1 (MQ=17)

     cGTAAAACTGCCGTTGAAGCAGCTATCGCGCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGAGCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCaa                                                                                                                                          <  1:414566/143‑1 (MQ=255)

        aaaaCTGCCGTGGAAGCAGCTATCGCCCGCGCCAAAACGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCCATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCt                                                                                                                                       <  1:169203/143‑1 (MQ=255)

         taaCCGCCGGTGAGGCAGCTGTCGCCCGCGCCAGAGCGCGCATGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTg                                                                                                                                      <  2:318506/142‑1 (MQ=14)

            cTGCGGTCGAAGCAGCTAACGCCCGCGCAAAAGCGCGTGAGCTGGAACAACAACAGGCAAATGCGGAACCAGAAGAACAGGTCGATCCACGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGaa                                                                                                                                   <  2:530583/143‑1 (MQ=11)

                cGTTGAAGCAGCTATCGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCACAGCGGCCGTCGAGGCCGCTATTGCACGAGCCAAAGCACGCAAGCTGGAACCGc                                                                                                                               >  2:457633/1‑143 (MQ=14)

                            tATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAGGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGACCAGCCACAGGCGAATg                                                                                                                   >  2:343868/1‑143 (MQ=11)

                            tATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATg                                                                                                                   <  1:526028/143‑1 (MQ=18)

                                 ccggcgcCACGGCGCGCAACCCGGAACAGCGCCAGGCAAATGCGGAACCAGCACACCTGGCCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGaa                                                                                                              <  2:458093/140‑1 (MQ=14)

                                 cccGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGaa                                                                                                              <  1:169992/143‑1 (MQ=40)

                                       cagcaGCGCGCAAACTGGAACAGCCACAGCCAACTGCCGACCCAGCACCCCTGGCCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCagaa                                                                                                        <  2:337418/139‑1 (MQ=14)

                                                    gCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCTGAACCAGGAGAACCGGTCGAta                                                                                           >  1:289250/1‑142 (MQ=255)

                                                              cAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCGAAGCGCGCAAGCAGGAACAGCAACGGGCTAATGCGGAGCCAGAAGAACAGGTCGAACCCCGCGAAgc                                                                                 >  2:525361/1‑143 (MQ=11)

                                                                     cTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCAAACGCCGCACCAGAGGAACAGGGCGATCCGCGCAGAGcggccggc                                                                          >  2:229885/1‑141 (MQ=11)

                                                                                ccAGAACACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTAt                                                               <  1:238890/143‑1 (MQ=255)

                                                                                                            ccgccgTCCAAGCCGCTATTGCCCGTGCCAAAGCGCGCACGCTGGTACGTCAACAGCCTAATGAGGATCCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGaa                                   <  1:229080/143‑1 (MQ=14)

                                                                                                             cgccgTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAAc                                  >  1:60888/1‑143 (MQ=255)

                                                                                                                         cGCTATTGCCCGTGTCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGACGCGGCTATTGCCCGCGCCCAAGCACGAAAAGTGGCACAGCAACAGGcga                      >  2:105204/1‑141 (MQ=14)

                                                                                                                                  ccGTGCCAAAGCGGGCACGCTGGAACAGCAACCTGCTGATGCGGCGCCACAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGcggtac             <  2:60888/143‑6 (MQ=11)

                                                                                                                                       ccAAGGCGCGCAAGCGGGAACAGCAGCAGGCGAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGaa        <  2:18090/143‑1 (MQ=255)

                                                                                                                                        cAAAGGACGCAAGCCGCAAAAGCAAGAGGCTAACGAGGCAACAGAAGAACGGGGCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGaac       <  1:221241/143‑1 (MQ=14)

                                                                                                                                        cAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGaac       <  1:323044/143‑1 (MQ=255)

                                                                                                                                             cgcgcAAGGTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAg  <  1:343868/143‑1 (MQ=255)

ATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAG  >  NC_000913/1708576‑1708859

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A