BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237271.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,894,514 number of mapped reads = 2,662,528 (91.99%) number of supplementary alignments = 19,093 (0.66%) number of secondary alignments = 0 number of mapped bases = 184,558,522 bp number of sequenced bases = 184,429,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,733 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2731 >>>>>>> ACTG content number of A's = 53,642,133 bp (29.09%) number of C's = 35,060,519 bp (19.01%) number of T's = 57,179,079 bp (31%) number of G's = 38,545,040 bp (20.9%) number of N's = 3,129 bp (0%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,493,155 number of insertions = 13,427 mapped reads with insertion percentage = 0.5% number of deletions = 73,386 mapped reads with deletion percentage = 2.71% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.4578X There is a 4.4% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14170726 0.05685332274458004 0.529254509830202 chr2 243199373 17145283 0.07049887830097325 0.49137690427075287 chr3 198022430 7815187 0.03946617057471722 0.25184080507900025 chr4 191154276 8956458 0.04685460449757347 0.2946590858754443 chr5 180915260 8668605 0.04791527812523941 0.2798344360293377 chr6 171115067 13218374 0.07724845176842317 0.3758048852640671 chr7 159138663 12048488 0.0757106272785514 0.6872438271716311 chr8 146364022 7024006 0.04798997666243416 0.9822897779030614 chr9 141213431 7911988 0.05602857988770204 0.38073103522914964 chr10 135534747 9566808 0.07058564841678569 0.4318310013064238 chr11 135006516 11032722 0.0817199223184161 0.49864040864654396 chr12 133851895 7485334 0.05592251047323611 0.30823068434521056 chr13 115169878 7693428 0.06680069592502304 0.33518569246919716 chr14 107349540 4192549 0.03905511844764309 0.26263738809961873 chr15 102531392 6691156 0.0652595841086406 0.3291950535503014 chr16 90354753 6446245 0.07134372886836401 0.36336988886086513 chr17 81195210 7383723 0.09093791370205213 0.45024531163291776 chr18 78077248 3622681 0.046398676859102414 0.6157064233601172 chr19 59128983 2692945 0.045543570400999454 0.5070164880947313 chr20 63025520 2740673 0.04348513110244866 0.2743822359232108 chr21 48129895 4512441 0.09375547152139019 0.41228809299931307 chr22 51304566 3438113 0.06701378197020515 0.3293309138330734 chrMT 16571 68734 4.147848651258222 3.1322708156282113 chrX 155270560 9719427 0.06259671505016791 0.34887020688566767 chrY 59373566 312428 0.005262072350513695 0.14092823031595597