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
A5 F13 I0 R1	213	60.4	2554362	98.6%	2518600	147.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	1,747,351	T→G	27.6%	E53A (GAG→GCG)	PP_5473 ←	LuxR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	1,747,351	0	T	G	27.6%	32.9 / 3.9	32	E53A (GAG→GCG)	PP_5473	LuxR family transcriptional regulator
Reads supporting (aligned to +/- strand): ref base T (2/21); new base G (2/7); total (4/28)
Fisher's exact test for biased strand distribution p-value = 5.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCTT  >  NC_002947_CJ‑RC/1747203‑1747496

ggTGCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCt                                                                                                                                                   >  1:148553/1‑149 (MQ=255)

        ccAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGgcgcg                                                                                                                                           <  8:38526/149‑1 (MQ=255)

         cAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGgcgcgc                                                                                                                                          <  2:148553/149‑1 (MQ=255)

             aGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCgcggcg                                                                                                                                      <  4:255197/149‑1 (MQ=255)

                  cTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGGGGCGGGCCGGCCCGccgcgggggg                                                                                                                                 >  4:229121/1‑145 (MQ=21)

                     tAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGGGGGGCGGCCGCGCCcggcggggggggc                                                                                                                              >  7:101318/1‑142 (MQ=21)

                              cACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATgggg                                                                                                                      <  6:224340/148‑1 (MQ=255)

                                    ctctTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCt                                                                                                                 <  5:283913/147‑1 (MQ=255)

                                         ggAAGGCCGGGTGCTTTGTTGTCTGCATGTATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGGGCGCCGCGCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGtt                                                                                                           <  1:150589/148‑1 (MQ=255)

                                         ggAAGGCCGGGTGCTTTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAAGGATTCGAACTTGGGGGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGtt                                                                                                           <  4:260697/148‑1 (MQ=255)

                                          gAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTg                                                                                                          <  4:167331/148‑1 (MQ=255)

                                           aaGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGACGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGAt                                                                                                        <  4:217274/149‑1 (MQ=255)

                                                      cATTGTTGTCTGAATGTATGATCCTCGGGTGGGTCAGGCTGGGTATTCGAAGGCCTCGGCCTTACTAACTATTCCAACTTGGGCGGTGCGCCGCGCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGgcatgca                                                                                             <  3:229434/149‑1 (MQ=18)

                                                           ttgtCTGCATGGTTGTTCGTCGGGTGGGTCTGGCGTGGTATTCGATGGCCTCGGCGTTACGAACGATTCTAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTGGGGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGc                                                                                         <  5:56074/148‑1 (MQ=17)

                                                           ttgtCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGc                                                                                         <  7:246834/148‑1 (MQ=255)

                                                             gtCTGCATGGATGATCCTGGGGTGGGTCTGGCGTGGTATTCGAAGGCCTCGGCATTACGAACGTTTCGAACTTGGGGGGTGCGCCGCTCGGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCca                                                                                       <  5:258214/148‑1 (MQ=18)

                                                              tCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCcac                                                                                      <  2:216254/148‑1 (MQ=255)

                                                                  cATGGATGATCCTCGGGTGGGGCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAaga                                                                                  <  1:184843/148‑1 (MQ=255)

                                                                          atCCTCGGGTGGGTCAGGCGTGGTATTCTACGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGGCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAgg                                                                         <  8:288520/149‑1 (MQ=255)

                                                                                gggtgggtCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAg                                                                    <  2:186828/148‑1 (MQ=255)

                                                                                         tggggTGGTATTCGACGGCCTCGGCCTTACTAACGATTCGAAGTTGGGGGGTGCGCGGCTCGGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGa                                                          <  5:211101/145‑1 (MQ=25)

                                                                                             gTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCGCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGtga                                                      <  7:197989/149‑1 (MQ=255)

                                                                                                      gAAGGCCTCGGCCTTACGAACGATGCGCACTTGGGCGGTGCGCCGCGCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGAtcttc                                              <  7:146894/148‑1 (MQ=255)

                                                                                                        tggCCTCGGCCTTACTAACGATTCGAAGTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGAtcttct                                             <  1:230893/146‑1 (MQ=255)

                                                                                                                           gaTTCGAACTTGGGCGGTGCGCCGCGCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACga                        <  5:74553/149‑1 (MQ=255)

                                                                                                                           gaTCCGAAGTGGGGGGGGGCGCCGGGCGGGCGGGGGGGGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACga                        <  3:21774/149‑1 (MQ=255)

                                                                                                                             ttCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACgaga                      <  8:101318/149‑1 (MQ=255)

                                                                                                                               cGACCTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGc                    <  3:229121/149‑1 (MQ=255)

                                                                                                                               cGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGagag                     <  4:251243/148‑1 (MQ=255)

                                                                                                                               cGAACTTGGGCGGGGCGCCGCGCCGGCGCGCGGCGGTCGCGGCGCATGGGGGCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGagag                     <  7:18744/148‑1 (MQ=255)

                                                                                                                                   cTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGtt                <  7:209635/149‑1 (MQ=255)

                                                                                                                                               gccgcTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAAcc    >  7:252345/1‑149 (MQ=255)

                                                                                                                                                   cTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCtt  >  1:109087/1‑147 (MQ=255)

GGTGCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGCTCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCTT  >  NC_002947_CJ‑RC/1747203‑1747496

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A