BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006092.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,862,722 number of mapped reads = 6,951,196 (88.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,510,371 number of mapped paired reads (second in pair) = 3,440,825 number of mapped paired reads (both in pair) = 6,390,560 number of mapped paired reads (singletons) = 560,636 number of mapped bases = 268,297,039 bp number of sequenced bases = 268,269,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 473,941 duplication rate = 6.19% >>>>>>> Insert size mean insert size = 65,312.7406 std insert size = 2,522,275.0636 median insert size = 93 >>>>>>> Mapping quality mean mapping quality = 46.5039 >>>>>>> ACTG content number of A's = 69,566,978 bp (25.93%) number of C's = 61,159,953 bp (22.8%) number of T's = 72,208,669 bp (26.92%) number of G's = 65,322,804 bp (24.35%) number of N's = 11,199 bp (0%) GC percentage = 47.15% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 1,005,729 number of insertions = 8,347 mapped reads with insertion percentage = 0.12% number of deletions = 21,350 mapped reads with deletion percentage = 0.31% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0867X std coverageData = 0.5079X There is a 5.01% of reference with a coverageData >= 1X There is a 2.04% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 22884555 0.09181343223213073 0.5349138715180145 chr2 243199373 23319478 0.09588625871991865 0.5395273486214057 chr3 198022430 18152395 0.09166837817311907 0.47161666123839746 chr4 191154276 15793883 0.08262374941589065 0.46726598417557 chr5 180915260 15919798 0.08799588271326587 0.4649496881675959 chr6 171115067 14936211 0.08728752681959911 0.5088998435634993 chr7 159138663 14772414 0.09282730997934802 0.6055676941434125 chr8 146364022 13263358 0.09061897738776269 0.5128430182213862 chr9 141213431 11639934 0.08242795262158881 0.47395471668296796 chr10 135534747 12960393 0.09562413541082568 0.498805704745443 chr11 135006516 12673854 0.09387586892472656 0.7221766052132378 chr12 133851895 12402339 0.09265717904105877 0.48104476402934165 chr13 115169878 7966330 0.06917025647973683 0.4144952875261248 chr14 107349540 8220331 0.0765753723770032 0.4395585136329985 chr15 102531392 8411653 0.0820397815334449 0.45630163777044885 chr16 90354753 8981028 0.09939740524773501 0.5288758913624448 chr17 81195210 8611781 0.10606267290890682 0.5536652519108097 chr18 78077248 6894596 0.08830480295616977 0.537032191658043 chr19 59128983 6653389 0.11252331196022769 0.6259487288144893 chr20 63025520 6770832 0.10743000613084985 0.5322386868202514 chr21 48129895 3552664 0.07381408166379752 0.47705506182286944 chr22 51304566 4105548 0.08002305291891564 0.5052545572282197 chrMT 16571 9930 0.5992396355078149 1.2249678200359195 chrX 155270560 7757735 0.04996269093123642 0.3479575625080264 chrY 59373566 1642610 0.02766567869613895 0.2724415724147851