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	5,991,726	Δ1 bp	12.5%	intergenic (+205/‑341)	kefB‑III → / → PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	5,991,726	0	A	.	12.5%	107.8 / 12.2	40	intergenic (+205/‑341)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
Reads supporting (aligned to +/- strand): ref base A (21/12); new base . (2/3); total (24/16)
Fisher's exact test for biased strand distribution p-value = 3.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01

CGCGGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTCGCCGCCATGACGCGAACTCACAA  >  NC_002947_CJ‑RC/5991588‑5991872

cgcgGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGaaacaaac                                                                                                                                           <  5:276453/148‑1 (MQ=255)

cgcgGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGaaacaaac                                                                                                                                           <  2:55570/148‑1 (MQ=255)

 gcgGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACg                                                                                                                                          >  5:288077/1‑148 (MQ=255)

 gccggTAAACCCCCTCCTACCTTTGTTTGGGGCCAGTTATTCCTGTGGGACGCCCACGCGACCCCCCAGGCGCCCCCCACCAAATCGCGGCCTACAAACAAGGCGGTCCCCCGCGCCTCGCACACGAGCGATTCGCCACAAACCAACg                                                                                                                                          >  8:64067/4‑148 (MQ=255)

   gggTAAACCCGCTCCTTCGTTTGTTTCGGGACAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACTAGGCGGTCGCGCGCGCCTGGCACTGGAGGGATTGGCCAGAAACAAACGTAg                                                                                                                                       <  4:179068/149‑1 (MQ=255)

    ggTAAACCCGCTACAACCTTTGTTTAGGGCCAGTTATTGCTGTGGGCCGCGCACGCCAGCCCCCTGGCCCCCGCCGGGATATCGCGGCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGGGGGATTGGCCAGAAACAAACCTAgg                                                                                                                                      >  4:105855/1‑149 (MQ=21)

         aCCCGCTCCTACGTTTGTTTCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCgg                                                                                                                                 <  8:287285/149‑1 (MQ=255)

              cTCCTACGTTTGTTTCGGGCCAGTTATTCCTGGGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGCCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTa                                                                                                                            <  1:199809/149‑1 (MQ=255)

                 cTACGTTTGTTTCGGGCCAATTATTCCTGCGGGATTTGCGCGCGACCGCCGTGGGGCATGTGTCGATATGGCGTCGTTCAAACAAGGCGGTCGCGCGCGAAGGGTGGAGGAGGGCCTGGCC‑GAAACAAACGTAGGAGCGGGTTTACCcg                                                                                                                        >  5:303129/1‑149 (MQ=2)

                      tttgtttCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTAcccgcg                                                                                                                      <  2:12809‑M2/147‑7 (MQ=255)

                      tttgtttCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTAcccgcg                                                                                                                      <  8:37755‑M2/147‑7 (MQ=255)

                           ttCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgcc                                                                                                               <  7:303733‑M2/149‑14 (MQ=255)

                                    gTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgccgcgcgggcg                                                                                                      <  7:271521‑M2/149‑23 (MQ=255)

                                      tATTCCTGCGGGATTTGCGCGCGACCGCCTTGGGGCATGTGACGATATGGCGTCGGAAAAACAAGGCGGTCGGGCGCGACTGGTGCAGGAGGGACTGGGC‑GAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGgcggcg                                                                                                   >  6:69795/1‑149 (MQ=12)

                                           cTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgccgcgcgggcggcgctc                                                                                                <  8:39686‑M2/148‑29 (MQ=255)

                                                                 cccTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCGCGATCTCATGGGCGCCCAAAAAc                                                                          >  7:290249/1‑148 (MQ=255)

                                                                    tGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATc                                                                      >  6:264374/1‑149 (MQ=255)

                                                                    tGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATc                                                                      >  4:53034/1‑149 (MQ=255)

                                                                            gCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCa                                                              >  5:70978/1‑149 (MQ=255)

                                                                                 gATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGACTGGTGCAGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctca                                                         <  2:284290‑M2/148‑68 (MQ=255)

                                                                                         gtcgtACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCAt                                                  >  5:296383/1‑148 (MQ=255)

                                                                                             tACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTg                                              >  5:123673/1‑148 (MQ=255)

                                                                                             tACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTg                                              >  3:150449/1‑148 (MQ=255)

                                                                                                aaacaaGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAAt                                          >  4:230110/1‑149 (MQ=255)

                                                                                                aaacaaGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAAt                                          >  3:228497/1‑149 (MQ=255)

                                                                                                  acaaGGCGGTCGCGCGCGACTGGTGCAGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctcaaaattccaacgccgtcca                                       <  7:191029‑M2/149‑86 (MQ=255)

                                                                                                    aaGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTcc                                      >  3:136815/1‑149 (MQ=255)

                                                                                                    aaGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCAGCAAtttac                                      >  4:235573/1‑147 (MQ=255)

                                                                                                               gcgcgcCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAACCGCCGCGCCGGCCGCGCTAGATGTCAATGGCGCCCAAAAACTATAGCCAGGCAACTGGAAGCCATACTGCAAATTGCTGACGATCAcc                           >  3:177440/1‑149 (MQ=25)

                                                                                                                   gcCCGGCACAGGAGGGTTTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTcgc                       >  6:248367/1‑149 (MQ=255)

                                                                                                                    ccTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTcgcc                      <  7:39686/149‑1 (MQ=255)

                                                                                                                     cTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTcgccg                     >  7:281327/1‑149 (MQ=255)

                                                                                                                      tGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTcgccgc                    <  3:53034/149‑1 (MQ=255)

                                                                                                                           caGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctcaaaattccaacgccgtccagtcaaaattccaacgccgccccct               <  7:97357‑M2/148‑110 (MQ=255)

                                                                                                                                ataattgGCCCGAAACAAACGTAGGAGCGGGTTTAcccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctcaaaattccaacgccgtccactcaaaattccaacgccgccccctcaaaa          >  2:33225‑M2/4‑35 (MQ=255)

                                                                                                                                   aTTGGCCAGAAACAAATGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTCGCCGCCATGACGCGAACt       >  6:116166/1‑149 (MQ=255)

                                                                                                                                       gCCCGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCCCAATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTCGCCGCCATGACGCGAACTca     <  1:55570/147‑1 (MQ=255)

                                                                                                                                       gCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTCGCCGCCATGACGCGAACTcac    >  4:102489/1‑148 (MQ=255)

                                                                                                                                        ccAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAAATTCCTGACGATCACCTCGCCGCCATGACGCGAACTcaca   >  2:219446/1‑148 (MQ=255)

                                                                                                                                         cAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTCGCCGCCATGACGCGAACTCACaa  >  5:139873/1‑148 (MQ=255)

CGCGGGTAAACCCGCTCCTACGTTTGTTTCGGGCCAGTTATTCCTGTGGGACGCGCACGCGAGCCCCCTGGCGCACGCCTCGATATCGCGTCGTACAAACAAGGCGGTCGCGCGCGCCTGGCACAGGAGGGATTGGCCAGAAACAAACGTAGGAGCGGGTTTACCCGCGAAGCGCCGCGCGGGCGGCGCTCGATCTCATGGGCGCCCAAAAACTATCGCCAGGCACCTGGAAGCCATCCTGCAATTTCCTGACGATCACCTCGCCGCCATGACGCGAACTCACAA  >  NC_002947_CJ‑RC/5991588‑5991872

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