BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238320.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 = 3,077,531 number of mapped reads = 2,802,923 (91.08%) number of supplementary alignments = 32,634 (1.06%) number of secondary alignments = 0 number of mapped bases = 186,032,884 bp number of sequenced bases = 185,951,129 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 157,723 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4222 >>>>>>> ACTG content number of A's = 52,669,637 bp (28.32%) number of C's = 34,758,557 bp (18.69%) number of T's = 58,399,548 bp (31.41%) number of G's = 40,064,574 bp (21.55%) number of N's = 58,813 bp (0.03%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,560,139 number of insertions = 14,381 mapped reads with insertion percentage = 0.51% number of deletions = 47,553 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.0601X std coverageData = 0.5425X There is a 4.69% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 14430409 0.05789517772154317 0.9847242054439759 chr2 243199373 14273494 0.058690504929879074 0.5692705639736916 chr3 198022430 12785074 0.06456376684196835 0.30991369604719154 chr4 191154276 12416800 0.0649569565474957 0.34636937659197664 chr5 180915260 11902608 0.06579106704431677 0.31791346591496006 chr6 171115067 10960161 0.06405140816734742 0.3968456523785228 chr7 159138663 10570215 0.06642141388356392 0.7271894087323145 chr8 146364022 9462470 0.06465024580972502 0.9811725238932725 chr9 141213431 7991700 0.056593058772150366 0.47669922437006484 chr10 135534747 8701942 0.06420450985901055 0.47483789419098377 chr11 135006516 8408061 0.062278927337107194 0.42824708252433413 chr12 133851895 8240050 0.06156095137838728 0.31796408280927696 chr13 115169878 6209933 0.053919767111327496 0.28572419829684237 chr14 107349540 5792637 0.05396051999850209 0.3388194226216168 chr15 102531392 5476064 0.053408657516324363 0.28701553732889296 chr16 90354753 5166287 0.05717781111083332 0.3309224781781853 chr17 81195210 4701175 0.057899659351826296 0.3463825969676753 chr18 78077248 5136060 0.06578177550520223 0.8929248915894659 chr19 59128983 3392985 0.05738277284424121 0.6592133739390368 chr20 63025520 3830680 0.06077982379201314 0.3210505616430406 chr21 48129895 2512315 0.052198638704696945 0.32744525934394647 chr22 51304566 1980201 0.03859697400032582 0.23776638378314643 chrMT 16571 16351 0.9867237945808943 1.2349535254780573 chrX 155270560 11174244 0.07196627615692247 0.37641793343903485 chrY 59373566 500968 0.008437559569859759 0.2171338165533522