BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237863.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 = 1,521,063 number of mapped reads = 1,012,599 (66.57%) number of supplementary alignments = 5,567 (0.37%) number of secondary alignments = 0 number of mapped bases = 61,164,125 bp number of sequenced bases = 61,131,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,757 duplication rate = 7.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8873 >>>>>>> ACTG content number of A's = 15,904,338 bp (26.02%) number of C's = 10,355,261 bp (16.94%) number of T's = 20,443,880 bp (33.44%) number of G's = 14,378,473 bp (23.52%) number of N's = 49,360 bp (0.08%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 563,979 number of insertions = 4,901 mapped reads with insertion percentage = 0.48% number of deletions = 20,993 mapped reads with deletion percentage = 2.05% homopolymer indels = 48.95% >>>>>>> Coverage mean coverageData = 0.0198X std coverageData = 0.2137X There is a 1.48% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 4961734 0.019906606371103083 0.27827304798424174 chr2 243199373 5320804 0.021878362326205505 0.2510674263026774 chr3 198022430 4280263 0.02161504128597957 0.1925684463361203 chr4 191154276 3971296 0.02077534483194088 0.19475652925308132 chr5 180915260 3839139 0.021220647722032956 0.18922390609597448 chr6 171115067 3492053 0.02040763014749601 0.20034243951313452 chr7 159138663 3517324 0.022102259335935227 0.25744809159157356 chr8 146364022 3213004 0.02195214340311036 0.2279589897349836 chr9 141213431 2694471 0.019080840830218198 0.2057971100267852 chr10 135534747 2694287 0.019878939236150268 0.22637915455143967 chr11 135006516 2617783 0.01939004929213935 0.20678330220420554 chr12 133851895 3150638 0.023538239783605603 0.20233724585006962 chr13 115169878 2115314 0.018366903193211683 0.17815644164261876 chr14 107349540 1722522 0.016045918780835017 0.17050819628104621 chr15 102531392 1817305 0.017724376549964328 0.17533410188515874 chr16 90354753 1529043 0.016922662607466814 0.1767502270545556 chr17 81195210 1375556 0.01694134419998421 0.1706674382705231 chr18 78077248 1684549 0.021575414645762105 0.3074018734618118 chr19 59128983 933784 0.015792323030484053 0.20910117706281553 chr20 63025520 1171706 0.018590977115301863 0.17936169136735047 chr21 48129895 847301 0.017604463919981543 0.17796991391029598 chr22 51304566 550173 0.010723665414107587 0.1326401196605443 chrMT 16571 38363 2.315068493150685 2.6823695656220465 chrX 155270560 3435953 0.022128811797935164 0.20109576310665053 chrY 59373566 189760 0.0031960350840304925 0.0896095781845755