BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083650.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,541,932 number of mapped reads = 1,143,485 (74.16%) number of supplementary alignments = 7,683 (0.5%) number of secondary alignments = 0 number of mapped bases = 73,393,626 bp number of sequenced bases = 73,368,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,086 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1586 >>>>>>> ACTG content number of A's = 22,367,564 bp (30.49%) number of C's = 13,714,962 bp (18.69%) number of T's = 21,144,987 bp (28.82%) number of G's = 16,137,139 bp (21.99%) number of N's = 4,342 bp (0.01%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 688,812 number of insertions = 5,543 mapped reads with insertion percentage = 0.48% number of deletions = 15,575 mapped reads with deletion percentage = 1.35% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2372X There is a 2.21% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6245688 0.025057863346306365 0.5070081266936944 chr2 243199373 7273197 0.029906314766691443 0.2357628951732406 chr3 198022430 6480218 0.03272466659458729 0.18933510577765617 chr4 191154276 4230097 0.02212923031865633 0.15635182959966729 chr5 180915260 2951518 0.01631436728996769 0.13328200118539282 chr6 171115067 5358102 0.03131285920017785 0.2111286947400492 chr7 159138663 3854187 0.024219048516198733 0.27011405645738984 chr8 146364022 4989736 0.03409127415205904 0.2942873206221314 chr9 141213431 3273245 0.023179416977695273 0.1825979322916661 chr10 135534747 3369473 0.024860584275115814 0.20953060808834956 chr11 135006516 3009331 0.02229026486395664 0.17360836193626739 chr12 133851895 2530289 0.01890364719901799 0.1451388496794819 chr13 115169878 2239578 0.019445865871282768 0.14477476773207026 chr14 107349540 1748781 0.016290530914245184 0.13453881850028904 chr15 102531392 2133144 0.020804789229819487 0.15087364769442102 chr16 90354753 2029893 0.022465813170890966 0.16117131412384197 chr17 81195210 1609817 0.01982650208060303 0.15168430667430524 chr18 78077248 2315013 0.02965028941593843 0.31510629304438625 chr19 59128983 1891903 0.03199620395974002 0.3319881036446716 chr20 63025520 1228557 0.01949300854637931 0.14671872542163816 chr21 48129895 1116537 0.023198409221545153 0.16047786460495264 chr22 51304566 690674 0.013462232581793987 0.12053169729316383 chrMT 16571 18219 1.099450847866755 1.2273534760212421 chrX 155270560 2648880 0.017059769733554126 0.14477260934603836 chrY 59373566 157549 0.0026535209288254644 0.06690260754710833