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
A3 F34 I0 R1	41	39.6	1695432	90.3%	1530975	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,708,973	T→C	20.3%	A685A (GCT→GCC)	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	1,708,973	0	T	C	20.3%	58.3 / 4.8	37	A685A (GCT→GCC)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
Reads supporting (aligned to +/- strand): ref base T (12/15); new base C (3/5); total (15/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCC  >  NC_000913/1708831‑1709111

aaCAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCt                                                                                                                                            >  1:660709/1‑143 (MQ=255)

     gCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGCTGATGCGCGCGAAGCTCCCGt                                                                                                                                       >  2:623533/1‑143 (MQ=255)

       tcaTGCCGAGCCAGACCGCCGGGCCGATCCGCGCAAAGCCGCCGTCGAAGCCGCGATCGCCCGAGCCAAAGCGCGCAAGCGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACGGGTTGATCCGCGCAAAGCTGCCGTCg                                                                                                                                     <  2:307589/141‑1 (MQ=17)

         aTGCGGCGCCAGAGCTACACGCCGATGCGCGCACTGCTGCCGTCGAAGCCGCTCTTCCGCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGaa                                                                                                                                   <  2:189313/143‑1 (MQ=18)

                gCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGCACAGCAACCGGCTAATGCGGAGCCAGAAGCACAGCTCGATCCGCGCAAAGCCGCCGACGACGCGGcca                                                                                                                            >  2:427875/1‑141 (MQ=14)

                 ccAGAACAACAGGGCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGCCGACGCGGCTAt                                                                                                                           >  2:217213/1‑143 (MQ=255)

                   agaagaACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGCGGACGCCCCACAGGCTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTg                                                                                                                         >  1:835776/1‑143 (MQ=17)

                      acaacaGGTCGATCCGCCCAAACCCTCCGTCGAAGCCGCTAGTGCCCGAGCCAAAGCGCGCAAGCGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCAc                                                                                                                      <  1:149856/143‑1 (MQ=25)

                            ggTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCa                                                                                                                <  1:29132/143‑1 (MQ=255)

                              tCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCGCGCAAGCGGGAACAGCAACCGGCTAATGCGGACCCAGAAGAAGAGGTCGATGCGCGCAAAGCCGCCGACGAAGCGGCGATTGCACGCGCCaaa                                                                                                              >  2:29132/1‑143 (MQ=11)

                                  tCCTCGCACACCCGCCGCCGAAGCGGCTACCGCCCGAGCCAAAGCGCGCAAGCGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGCACAGGTTGATCCGCGCGAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCAc                                                                                                          <  2:141381/143‑1 (MQ=255)

                                      cgcAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAATCCGCTATTGCACGCGCCCAACCACGCaa                                                                                                      >  2:237253/1‑143 (MQ=255)

                                          aaGCCGCCGTGGAGGCCGCTGTGGCCCGAGCCAAAGCGCGCAAACGGGACCAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTg                                                                                                  <  2:835776/143‑1 (MQ=37)

                                          aaGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTg                                                                                                  <  1:228003/143‑1 (MQ=255)

                                               gccgTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACa                                                                                             <  1:196782/143‑1 (MQ=255)

                                                ccgTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAg                                                                                            <  1:271936/143‑1 (MQ=255)

                                                            cccgagCCCGACCCAGTGCGCGCAACCTTTAACCGCAACGAGCCAATGCCGAGCTAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAAt                                                                                <  2:773486/138‑1 (MQ=14)

                                                                 gCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGt                                                                           <  1:765248/143‑1 (MQ=255)

                                                                  cccGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTa                                                                          >  2:34061/1‑143 (MQ=255)

                                                                   ccGGGCCACCGCCCGCAACCGGGAACAGCAGCCGGCTAATGCCGAGCCAGAAGCACAGGTGGACCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTAc                                                                         <  2:322876/143‑1 (MQ=14)

                                                                                       gggAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCCAGGTGGAACAACAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCcg                                                     >  2:594676/1‑143 (MQ=255)

                                                                                             aGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCaaa                                               >  1:723889/1‑143 (MQ=255)

                                                                                                aaCCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCCGGCGGAGAGGCGCGCCAGCTGGAACAGCAACAGGCCAAGGCGGTACCGGAGGAACAGGTTGAACCACGCCAAGCg                                            >  2:252704/1‑143 (MQ=17)

                                                                                                aaCCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCCCCACGACAATGCGGTACGAGAGGAACAGGTTGATCCGCGCAAAGCg                                            >  1:572048/1‑143 (MQ=18)

                                                                                                  ccGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACGAGAAGAACCGGTTGATCCGCGCAAAGCGGc                                          >  1:829951/1‑143 (MQ=255)

                                                                                                   cGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCAAACGTGTTAGCTGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCa                                         <  1:614100/143‑1 (MQ=18)

                                                                                                        aaTGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCGGCTCACGCTCGTGCCAAAGCACGCCAGCTGCAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGc                                    <  2:267242/143‑1 (MQ=11)

                                                                                                             ggAGCCAGAACAACAGGTGGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGGACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCgg                               <  1:588618/143‑1 (MQ=255)

                                                                                                                 ccAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGGACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGATGATACGCGCAAAGCGGCAGTTGCCGCGACTac                           >  2:40666/1‑142 (MQ=255)

                                                                                                                        aaCAGGTGGACCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCcgc                    <  1:260386/143‑1 (MQ=255)

                                                                                                                             gTTGACCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCa               <  1:671030/143‑1 (MQ=255)

                                                                                                                              ttGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGCTCCGCGCAAAGCGGCAGTCGCCGCGGCTAGTGACCGCGCTCAg              >  2:226711/1‑143 (MQ=255)

                                                                                                                               tGATCCGCGCACAGCCGCCGTCGACGCCGCTGTTGCCCGCGCCCAAGCACGCAAGGTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAgg             <  2:97213/143‑1 (MQ=18)

                                                                                                                               tGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAgg             <  1:740805/143‑1 (MQ=255)

                                                                                                                               tGATCCGCGCAAAGCGGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAgg             <  1:740766/143‑1 (MQ=255)

                                                                                                                                gATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGc            <  1:354722/143‑1 (MQ=255)

                                                                                                                                 aTCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGcc           >  1:32124/1‑143 (MQ=255)

                                                                                                                                          aaGCCGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAgcc  <  2:32124/143‑1 (MQ=255)

AACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCC  >  NC_000913/1708831‑1709111

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