BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617374.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,580,675 (95.56%) number of supplementary alignments = 67,394 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,354,621 number of mapped paired reads (second in pair) = 15,226,054 number of mapped paired reads (both in pair) = 30,141,338 number of mapped paired reads (singletons) = 439,337 number of mapped bases = 3,006,010,395 bp number of sequenced bases = 3,005,116,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,582,180 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 58,125.4548 std insert size = 2,312,100.947 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 53.5116 >>>>>>> ACTG content number of A's = 908,772,036 bp (30.24%) number of C's = 596,718,647 bp (19.86%) number of T's = 897,329,222 bp (29.86%) number of G's = 600,115,302 bp (19.97%) number of N's = 2,180,860 bp (0.07%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 29,802,657 number of insertions = 304,024 mapped reads with insertion percentage = 0.96% number of deletions = 369,223 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.971X std coverageData = 9.8607X There is a 53.63% of reference with a coverageData >= 1X There is a 24.37% of reference with a coverageData >= 2X There is a 9.41% of reference with a coverageData >= 3X There is a 3.31% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 195244510 0.7833260724353421 19.94746995178229 chr2 243199373 296593446 1.219548563556535 8.942957947724995 chr3 198022430 239155277 1.2077181206189622 1.4668729964633715 chr4 191154276 164411098 0.8600963653044309 9.570381491442168 chr5 180915260 188623603 1.0426074782193608 1.4657752565562525 chr6 171115067 141020031 0.8241239855284047 3.68300954170598 chr7 159138663 244297803 1.5351253956431694 11.128534442237184 chr8 146364022 126558780 0.8646850385130849 7.839622695872776 chr9 141213431 126711383 0.8973040461002608 15.049436454394074 chr10 135534747 126345161 0.9321975640682016 20.076870994569997 chr11 135006516 160964966 1.1922755343156919 5.5810693558892925 chr12 133851895 133118569 0.9945213625851169 1.3490585988409292 chr13 115169878 130799847 1.1357122997039208 1.2962202276341852 chr14 107349540 86931470 0.8097982534438434 1.3871005865411954 chr15 102531392 67505668 0.6583902420831271 0.9807120337187298 chr16 90354753 75465075 0.835208691235092 7.916761752402222 chr17 81195210 93749318 1.1546163622213674 7.12948017825069 chr18 78077248 54518701 0.6982661709593043 15.619481096681765 chr19 59128983 55962433 0.94644673661984 9.67236404082171 chr20 63025520 86381638 1.3705819166585218 2.514085901061589 chr21 48129895 47836022 0.9938941691021765 3.358554320568716 chr22 51304566 26821185 0.522783586162682 0.9192917977036295 chrMT 16571 2063409 124.51928067105183 20.953121462649058 chrX 155270560 124665273 0.8028905994800302 2.9428656287180743 chrY 59373566 10265729 0.1729006642450952 8.52549784245154