BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234135.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 = 1,539,183 number of mapped reads = 752,779 (48.91%) number of supplementary alignments = 2,614 (0.17%) number of secondary alignments = 0 number of mapped bases = 44,288,624 bp number of sequenced bases = 44,257,873 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,073 duplication rate = 5.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0888 >>>>>>> ACTG content number of A's = 11,679,121 bp (26.39%) number of C's = 7,025,953 bp (15.88%) number of T's = 14,687,757 bp (33.19%) number of G's = 10,862,079 bp (24.54%) number of N's = 2,963 bp (0.01%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 473,060 number of insertions = 3,724 mapped reads with insertion percentage = 0.49% number of deletions = 17,420 mapped reads with deletion percentage = 2.28% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.1674X There is a 1.21% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 3862762 0.015497502010235713 0.1989251633749835 chr2 243199373 3154437 0.012970580314777373 0.17065196803107688 chr3 198022430 3741010 0.018891849776815687 0.16422235305532235 chr4 191154276 2265938 0.011853974953717488 0.13245538731344783 chr5 180915260 2666656 0.014739806912916025 0.14471958018775316 chr6 171115067 2911565 0.017015246237784543 0.17126925548628094 chr7 159138663 2667513 0.016762193107026417 0.20991398303099998 chr8 146364022 2231988 0.015249567274121505 0.2692514732238003 chr9 141213431 1753146 0.012414867251543516 0.1458420492353798 chr10 135534747 2180086 0.016085070790001918 0.1607050788632665 chr11 135006516 2089628 0.015477978855479834 0.17068246734043432 chr12 133851895 1714360 0.012807887404208958 0.1334522382434297 chr13 115169878 1721106 0.014944063759449323 0.14746212489587177 chr14 107349540 1804957 0.01681383078120316 0.15487513049691373 chr15 102531392 1033568 0.01008050295464632 0.11798277149993269 chr16 90354753 1175179 0.013006277600028412 0.13540352701624442 chr17 81195210 1060426 0.013060203920896319 0.13758059432191133 chr18 78077248 1024806 0.013125539465735268 0.23100339751193089 chr19 59128983 1020450 0.017258034016921955 0.17105634368091574 chr20 63025520 999420 0.015857386023947127 0.15087114275904667 chr21 48129895 685364 0.014239881470757417 0.14037108718797398 chr22 51304566 410104 0.00799351854959654 0.10555573487088336 chrMT 16571 33491 2.021060889505763 2.476641317228762 chrX 155270560 1917882 0.012351871468744622 0.1354305476004935 chrY 59373566 162782 0.0027416577943120343 0.06317445145626749