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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	379,606	C→T	92 (TAG→TAA)	frmR ←	regulator protein that represses frmRAB operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	379,606	0	C	T	97.1%	105.4 / ‑4.4	35	92 (TAG→TAA)	frmR	regulator protein that represses frmRAB operon
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (17/17); minor base A (1/0); total (18/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

ACTTCACCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGCTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGCCCATTAGCCGC  >  NC_000913/379483‑379740

aCTTCACCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCTGTTATTTAAGATAGGCa                                                                                                                         <  2:503375/139‑1 (MQ=255)

     aCCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAAc                                                                                                                    <  1:172028/139‑1 (MQ=255)

     aCCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAAc                                                                                                                    <  1:342302/139‑1 (MQ=255)

     aCCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAAc                                                                                                                    <  1:356558/139‑1 (MQ=255)

     aCCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAAc                                                                                                                    <  1:368546/139‑1 (MQ=255)

                             aaTTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGa                                                                                            <  1:686546/139‑1 (MQ=255)

                                   aaCGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCa                                                                                                                  >  2:313321/1‑111 (MQ=255)

                                   aaCGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCa                                                                                                                  <  1:313321/111‑1 (MQ=255)

                                                                aTGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGt                                                         <  2:678710/139‑1 (MQ=255)

                                                                aTGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGt                                                         <  1:472298/139‑1 (MQ=255)

                                                                           gcaCGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTcc                                              >  2:535168/1‑139 (MQ=255)

                                                                            caCGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTTAGTTAGTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCaa                                                                                                <  2:538033/88‑1 (MQ=255)

                                                                            caCGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCaa                                                                                                >  1:538033/1‑88 (MQ=255)

                                                                             aCGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCg                                            >  1:162332/1‑139 (MQ=255)

                                                                                      cATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGa                                                                                                                               >  1:397882/1‑47 (MQ=255)

                                                                                      cATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGa                                                                                                                               <  2:397882/47‑1 (MQ=255)

                                                                                            tcGCTCTTCCTCAATATGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAg                             <  2:115053/139‑1 (MQ=255)

                                                                                                            tGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAgtgt                                                                                                      <  2:135734/50‑1 (MQ=255)

                                                                                                            tGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAgtgt                                                                                                      >  1:135734/1‑50 (MQ=255)

                                                                                                            tGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCa                                                                    >  1:186165/1‑84 (MQ=255)

                                                                                                            tGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCa                                                                    <  2:186165/84‑1 (MQ=255)

                                                                                                            tGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGc             >  1:52508/1‑139 (MQ=255)

                                                                                                            tGGTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGc             >  1:332794/1‑139 (MQ=255)

                                                                                                              gTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCt                                                                                      >  2:766880/1‑64 (MQ=255)

                                                                                                              gTAATAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCt                                                                                      <  1:766880/64‑1 (MQ=255)

                                                                                                              gTAATAGATGCAGATATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCCCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGccc           >  1:541182/1‑139 (MQ=255)

                                                                                                                  tAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAg                             <  2:167481/117‑1 (MQ=255)

                                                                                                                  tAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAg                             >  1:167481/1‑117 (MQ=255)

                                                                                                                  tAGATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGCCCATTa       >  1:752143/1‑139 (MQ=255)

                                                                                                                    gATTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGCCCATTAGc     >  2:134477/1‑139 (MQ=255)

                                                                                                                     aTTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGc                                                                           <  2:102752/68‑1 (MQ=255)

                                                                                                                     aTTCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGc                                                                           >  1:102752/1‑68 (MQ=255)

                                                                                                                       tCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGCCCATTAGCcgc  >  2:196283/1‑139 (MQ=255)

                                                                                                                       tCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGCCCATTAGCcgc  >  1:695460/1‑139 (MQ=255)

                                                                                                                       tCAGTTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACGTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTATCACGACTATGGCTATCAAGCACTTCTGCCATCACCCCATTAGCcgc  >  1:701880/1‑139 (MQ=255)

ACTTCACCTTTTTTCGGTGGTGCAACGTCAATTTCAACGATTTCCAGCGGTTTACCGGGAGCAAATGCAACGGCAGCACGTGATTTCATCTCTCGCTCTTCCTCAATATGGTAATAGATTCAGCTATTTAAGATAGGCACGAACCAGTTCAATAGTGTCGTCAACGGATTGGCTGACTTCGCGGCTGTAGCAGTCATTTCGGTCAAACGTTTCCCGGATATGGCTTTCAAGCACTTCTGCCATCAGCCCATTAGCCGC  >  NC_000913/379483‑379740

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A