BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926941.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 7,673,208 number of mapped reads = 7,518,117 (97.98%) number of supplementary alignments = 165,361 (2.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,763,700 number of mapped paired reads (second in pair) = 3,754,417 number of mapped paired reads (both in pair) = 7,426,974 number of mapped paired reads (singletons) = 91,143 number of mapped bases = 700,973,102 bp number of sequenced bases = 700,452,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,178 duplication rate = 3.62% >>>>>>> Insert size mean insert size = 242,888.5592 std insert size = 4,734,287.46 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 51.5663 >>>>>>> ACTG content number of A's = 199,761,932 bp (28.52%) number of C's = 139,594,050 bp (19.93%) number of T's = 202,311,946 bp (28.88%) number of G's = 158,636,509 bp (22.65%) number of N's = 148,358 bp (0.02%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 6,262,914 number of insertions = 115,345 mapped reads with insertion percentage = 1.51% number of deletions = 359,377 mapped reads with deletion percentage = 4.66% homopolymer indels = 52.66% >>>>>>> Coverage mean coverageData = 0.2264X std coverageData = 0.9959X There is a 13.95% of reference with a coverageData >= 1X There is a 5.09% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% 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 6117734 0.024544508557112082 0.7816706076981274 chr2 243199373 85461987 0.3514071025174888 1.9539304264961328 chr3 198022430 66223405 0.33442375694510973 0.8169590337330837 chr4 191154276 32690032 0.17101386735392726 0.8966791961878701 chr5 180915260 28530968 0.157703490573432 0.5438402950502189 chr6 171115067 55271339 0.3230068512903075 0.8962216890594679 chr7 159138663 32179805 0.20221236243514248 0.6705145804766348 chr8 146364022 22941180 0.15674056838913597 0.5716289124055998 chr9 141213431 42321710 0.29970031674961567 1.1079219336077066 chr10 135534747 35616387 0.26278417740359966 0.969385410793751 chr11 135006516 46089803 0.3413894704163761 1.5265973098945693 chr12 133851895 43484732 0.32487199378088744 0.8232188027654956 chr13 115169878 3922796 0.03406095472290072 0.24742311773451503 chr14 107349540 30343591 0.28266158383165874 0.7705317553122943 chr15 102531392 22672859 0.22113090008570252 0.6869973043819406 chr16 90354753 8811974 0.09752640240187475 0.9142907088617388 chr17 81195210 25501061 0.3140710024643079 1.0317570246494936 chr18 78077248 25931510 0.3321263321166238 1.0793885045983025 chr19 59128983 15367234 0.2598934265451513 0.9437254075004439 chr20 63025520 9271432 0.14710599769744065 0.554654280609776 chr21 48129895 3032065 0.06299754030213446 0.5525584569931837 chr22 51304566 1772542 0.034549400534837384 0.2758773053588251 chrMT 16571 81804 4.936575945929636 4.86080928314785 chrX 155270560 56157283 0.3616737326122866 0.9695556479744222 chrY 59373566 1177869 0.019838272809822474 0.7895651560378468