BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124868.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,327,684 number of mapped reads = 2,306,037 (99.07%) number of supplementary alignments = 687,673 (29.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,154,543 number of mapped paired reads (second in pair) = 1,151,494 number of mapped paired reads (both in pair) = 2,296,834 number of mapped paired reads (singletons) = 9,203 number of mapped bases = 309,156,254 bp number of sequenced bases = 308,735,132 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 855,819 duplication rate = 25.01% >>>>>>> Insert size mean insert size = 1,386,891.1545 std insert size = 11,115,138.2009 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 46.9601 >>>>>>> ACTG content number of A's = 91,139,651 bp (29.52%) number of C's = 63,204,457 bp (20.47%) number of T's = 90,188,642 bp (29.21%) number of G's = 64,177,475 bp (20.79%) number of N's = 24,907 bp (0.01%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0188 number of mismatches = 5,456,554 number of insertions = 118,843 mapped reads with insertion percentage = 4.79% number of deletions = 199,860 mapped reads with deletion percentage = 8.19% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0999X std coverageData = 4.824X There is a 4.48% of reference with a coverageData >= 1X There is a 2.6% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 25943789 0.10408715892427005 3.1227393561263757 chr2 243199373 26851743 0.110410412118949 3.496934667617702 chr3 198022430 17336397 0.08754764296145644 1.546414082590797 chr4 191154276 19988547 0.10456761636867595 2.795922043699034 chr5 180915260 15808099 0.08737847210898628 0.5007922130492075 chr6 171115067 15236093 0.08904004344632024 1.497931828826592 chr7 159138663 14575815 0.09159191566162649 2.6986259076689403 chr8 146364022 16421456 0.11219598761777673 1.0456774004595286 chr9 141213431 10435469 0.07389855855849858 3.4183620356453526 chr10 135534747 27922791 0.20601942762323525 19.902203972371947 chr11 135006516 10534786 0.0780316855224973 1.1924228575339288 chr12 133851895 13025860 0.09731546945973384 0.5169114755323986 chr13 115169878 7003862 0.06081331439805814 0.37681453599120923 chr14 107349540 7391486 0.0688543798138306 0.5017052646363837 chr15 102531392 6781604 0.06614173345076599 0.3903669765787659 chr16 90354753 16405765 0.18157058101857684 6.132296466405614 chr17 81195210 7113935 0.08761520537972622 3.2248327914807113 chr18 78077248 6725013 0.08613281298029357 3.00392431416338 chr19 59128983 4288309 0.07252465343434031 1.8705093565391222 chr20 63025520 7755589 0.12305474036549004 1.0714560828972906 chr21 48129895 3462049 0.07193136407216347 1.571469033360621 chr22 51304566 1414601 0.027572614102222403 0.36695632072156614 chrMT 16571 61896 3.7352000482771106 3.736327889721776 chrX 155270560 23479577 0.1512171850220673 1.4310307129343431 chrY 59373566 3191723 0.05375663304440902 5.228362638072596