BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038492.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 72,356,550 number of mapped reads = 71,911,407 (99.38%) number of supplementary alignments = 141,916 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 36,094,352 number of mapped paired reads (second in pair) = 35,817,055 number of mapped paired reads (both in pair) = 71,596,820 number of mapped paired reads (singletons) = 314,587 number of mapped bases = 10,675,202,657 bp number of sequenced bases = 10,673,381,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,994,667 duplication rate = 35.25% >>>>>>> Insert size mean insert size = 19,111.9827 std insert size = 1,449,498.1135 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 55.8402 >>>>>>> ACTG content number of A's = 2,659,874,312 bp (24.92%) number of C's = 2,675,749,871 bp (25.07%) number of T's = 2,679,022,313 bp (25.1%) number of G's = 2,658,329,442 bp (24.91%) number of N's = 405,830 bp (0%) GC percentage = 49.98% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 60,097,565 number of insertions = 547,674 mapped reads with insertion percentage = 0.73% number of deletions = 655,946 mapped reads with deletion percentage = 0.89% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 3.4484X std coverageData = 22.0569X There is a 23.1% of reference with a coverageData >= 1X There is a 14.41% of reference with a coverageData >= 2X There is a 9.13% of reference with a coverageData >= 3X There is a 7.09% of reference with a coverageData >= 4X There is a 5.66% of reference with a coverageData >= 5X There is a 4.92% of reference with a coverageData >= 6X There is a 4.42% of reference with a coverageData >= 7X There is a 4.11% of reference with a coverageData >= 8X There is a 3.89% of reference with a coverageData >= 9X There is a 3.72% of reference with a coverageData >= 10X There is a 3.59% of reference with a coverageData >= 11X There is a 3.49% of reference with a coverageData >= 12X There is a 3.4% of reference with a coverageData >= 13X There is a 3.32% of reference with a coverageData >= 14X There is a 3.25% of reference with a coverageData >= 15X There is a 3.19% of reference with a coverageData >= 16X There is a 3.13% of reference with a coverageData >= 17X There is a 3.07% of reference with a coverageData >= 18X There is a 3.02% of reference with a coverageData >= 19X There is a 2.97% of reference with a coverageData >= 20X There is a 2.92% of reference with a coverageData >= 21X There is a 2.87% of reference with a coverageData >= 22X There is a 2.83% of reference with a coverageData >= 23X There is a 2.79% of reference with a coverageData >= 24X There is a 2.74% of reference with a coverageData >= 25X There is a 2.7% of reference with a coverageData >= 26X There is a 2.67% of reference with a coverageData >= 27X There is a 2.63% of reference with a coverageData >= 28X There is a 2.59% of reference with a coverageData >= 29X There is a 2.56% of reference with a coverageData >= 30X There is a 2.52% of reference with a coverageData >= 31X There is a 2.49% of reference with a coverageData >= 32X There is a 2.45% of reference with a coverageData >= 33X There is a 2.42% of reference with a coverageData >= 34X There is a 2.39% of reference with a coverageData >= 35X There is a 2.36% of reference with a coverageData >= 36X There is a 2.33% of reference with a coverageData >= 37X There is a 2.3% of reference with a coverageData >= 38X There is a 2.27% of reference with a coverageData >= 39X There is a 2.24% of reference with a coverageData >= 40X There is a 2.21% of reference with a coverageData >= 41X There is a 2.19% of reference with a coverageData >= 42X There is a 2.16% of reference with a coverageData >= 43X There is a 2.13% of reference with a coverageData >= 44X There is a 2.11% of reference with a coverageData >= 45X There is a 2.08% of reference with a coverageData >= 46X There is a 2.05% of reference with a coverageData >= 47X There is a 2.03% of reference with a coverageData >= 48X There is a 2.01% of reference with a coverageData >= 49X There is a 1.98% of reference with a coverageData >= 50X There is a 1.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 924387806 3.7086680157157965 21.754567898163902 chr2 243199373 866161319 3.5615277634782387 23.00981979281276 chr3 198022430 608637206 3.0735770993215263 19.637134523414538 chr4 191154276 369049455 1.9306366706649032 14.299696330676433 chr5 180915260 466622722 2.5792336257317374 18.574246230428546 chr6 171115067 621793704 3.6337753004532325 23.706452225007137 chr7 159138663 696940529 4.379454469841813 29.188776015707976 chr8 146364022 338106655 2.310039382492509 16.095336291954975 chr9 141213431 421902199 2.987691723176105 19.43154787551016 chr10 135534747 340730803 2.5139738003864056 15.373143240950924 chr11 135006516 708869303 5.250630295503663 29.9123639977666 chr12 133851895 469433132 3.50710859939637 19.325825942012624 chr13 115169878 363671989 3.1577005664623523 25.68777157605868 chr14 107349540 260444549 2.426135677898573 15.31149609884902 chr15 102531392 284691170 2.7766244507828395 16.18779222236712 chr16 90354753 515083135 5.700675591465565 29.46298761398311 chr17 81195210 627768817 7.7315991546791984 32.978866037391896 chr18 78077248 110091211 1.4100293468335359 10.389161353914542 chr19 59128983 662227610 11.199712499705939 39.285154456845206 chr20 63025520 402868644 6.392151052462558 35.44763807509026 chr21 48129895 87966137 1.8276818804611978 19.672922454218693 chr22 51304566 177615289 3.4619781989774556 18.04186538592422 chrMT 16571 1408123 84.97513728803331 28.521120207703873 chrX 155270560 328872445 2.118060532531086 15.291542417185354 chrY 59373566 19858705 0.3344704779901547 4.518702964543019