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
A17 F104 I1 R1	25	31.6	1325236	90.2%	1195362	142.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,158,785	C→T	P99L (CCC→CTC)	oxyR →	DNA‑binding transcriptional dual regulator OxyR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,158,785	0	C	T	96.8%	81.4 / NA	31	P99L (CCC→CTC)	oxyR	DNA‑binding transcriptional dual regulator OxyR
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (16/14); minor base G (0/1); total (16/15)
Fisher's exact test for biased strand distribution p-value = 4.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATC  >  NC_000913/4158647‑4158924

gTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGAGCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACTACGTCCGGACCGCTGCACATTGGTTTGATTCTcaca                                                                                                                                         <  1:341489/143‑1 (MQ=255)

    aGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGCGATGGCAAGCCCGCAGGGCGAGAGGATGTCCGGACCGCTGCACATTGCTTTGATTCTCGCACTTg                                                                                                                                     >  2:498509/1‑143 (MQ=255)

        ttgttCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGAcc                                                                                                                                 >  1:573972/1‑143 (MQ=255)

          gttCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGGGAAAGTCCTTAAAGAGATGGCAAGCCAGCGGGGCGAGACGATGGCCGGACCGCTGCACACTGGTTTGATTCTCACAGTTGGACCGt                                                                                                                               >  2:13915/1‑143 (MQ=255)

          gttCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGGGCTGCGTGAGGTGAAAGTCCTGAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGCTTGTCACAGGTGGAGCGt                                                                                                                               >  2:400885/1‑143 (MQ=255)

            tCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTAc                                                                                                                             >  1:381568/1‑143 (MQ=255)

                 cAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGGCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTCTGATGCTCACAGTTGGACCGTACCTGcg                                                                                                                        >  2:521199/1‑142 (MQ=255)

                  aGGCGGGAATGCGGCTGGGGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTGAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTa                                                                                                                       <  1:231479/143‑1 (MQ=255)

                       ggAATGCTGCTCGTGGCTCATCCTCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCa                                                                                                                  <  1:620267/143‑1 (MQ=255)

                              tgctgGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATc                                                                                                           <  1:635819/143‑1 (MQ=255)

                                   gtggATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTAt                                                                                                      >  1:68747/1‑143 (MQ=255)

                                            gtgcgTACCGTGCTCCGAGAGCTGAAAGTCCTTTATGATATGGCAAGCTAGCAGCTCGAGACGATGTCCGGATCGCTGCACATTGTTTTGATTCTCACAGTTGGACCGTACTTGCTACCGCATATTATCCCTATGCTGCACCa                                                                                             <  2:13683/141‑1 (MQ=255)

                                            gcgcGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCa                                                                                             >  1:131905/1‑143 (MQ=255)

                                                 tACCGTGCTGCGTGCGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGGCGATGTCCGGACCGCTCCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCt                                                                                        <  1:212323/143‑1 (MQ=255)

                                                   ccGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCatt                                                                                      <  2:204921/143‑1 (MQ=255)

                                                        ctgcATGAGGTGACAGTCCTTAAAGAGATCGCTAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCaaa                                                                                 <  2:262010/143‑1 (MQ=255)

                                                          gcGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCCTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCACAGc                                                                               >  2:63355/1‑143 (MQ=255)

                                                            gggAGGGGGAAGGCATTAAAGAGAGGGCGAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTCGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTg                                                                             <  1:81671/141‑1 (MQ=255)

                                                                 gTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGAGGTCCGGACCGCTGCACATAGGTTTGATTCTCACCGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTGTCCAAAGCGGGaaag                                                                        >  2:597342/1‑142 (MQ=255)

                                                                         ccTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCGCCAGACCTTTCCAAAGCGGGAACTGTGTCTGc                                                                >  2:500817/1‑143 (MQ=255)

                                                                           ttAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCAt                                                              >  2:443748/1‑143 (MQ=255)

                                                                            tAAAGAGATGGCAAGCCAGCAGGGCGTGACGATGTGCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGACACGTATCTGCATg                                                             <  2:616003/143‑1 (MQ=255)

                                                                             aaaGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTACACAGTGGTTTGATTCTCACAGCTGGGCCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTACAACGCTGGAAGAGTATCTGCATGa                                                            >  1:518680/1‑143 (MQ=255)

                                                                              aaGAGACGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGaa                                                           <  1:213809/143‑1 (MQ=255)

                                                                               agagATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAg                                                          >  1:616640/1‑143 (MQ=255)

                                                                                  gaTGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGAAAATGTATCTGCATGACGctc                                                       >  1:330251/1‑141 (MQ=255)

                                                                                          gCCAGCAGGGCGAGGCGATGTCCGGACCGCTGCACATTGGTTTGATGCGCACAGTTGGACCGTACCTGCGACCGCCTATTATCCCCATGCTGCACCAGAGCTTTCCAAAGCTGGAAATGGATCTGCATGAAGCACAGACccac                                               <  2:9962/143‑1 (MQ=255)

                                                                                                          gATGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAACTGTATCTGCATGAAGCCCAGCCCCCCCCGTTCCTGGCGCCAc                               >  1:252036/1‑143 (MQ=255)

                                                                                                            tGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTg                             <  2:147491/143‑1 (MQ=255)

                                                                                                            tGTCCGGACCGCTGCACATTGGTTTGATTCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTg                             <  1:330109/143‑1 (MQ=255)

                                                                                                                                       ttCTCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATc  <  1:143970/143‑1 (MQ=255)

GTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATC  >  NC_000913/4158647‑4158924

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