BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124833.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 = 26,097,940 number of mapped reads = 25,716,801 (98.54%) number of supplementary alignments = 115,712 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,887,180 number of mapped paired reads (second in pair) = 12,829,621 number of mapped paired reads (both in pair) = 25,604,504 number of mapped paired reads (singletons) = 112,297 number of mapped bases = 2,225,441,035 bp number of sequenced bases = 2,224,127,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,302,499 duplication rate = 11.18% >>>>>>> Insert size mean insert size = 39,494.5902 std insert size = 1,847,639.4545 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.7887 >>>>>>> ACTG content number of A's = 619,455,946 bp (27.85%) number of C's = 417,849,412 bp (18.79%) number of T's = 653,463,531 bp (29.38%) number of G's = 533,338,287 bp (23.98%) number of N's = 20,722 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 16,556,392 number of insertions = 314,283 mapped reads with insertion percentage = 1.18% number of deletions = 744,822 mapped reads with deletion percentage = 2.84% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.7189X std coverageData = 5.7473X There is a 29.62% of reference with a coverageData >= 1X There is a 15.46% of reference with a coverageData >= 2X There is a 8.63% of reference with a coverageData >= 3X There is a 5.18% of reference with a coverageData >= 4X There is a 3.24% of reference with a coverageData >= 5X There is a 2.11% of reference with a coverageData >= 6X There is a 1.41% of reference with a coverageData >= 7X There is a 0.97% of reference with a coverageData >= 8X There is a 0.68% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% 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 139620433 0.5601608230296045 5.36800282563334 chr2 243199373 215930190 0.8878731360874027 9.889913241739766 chr3 198022430 141889836 0.7165341623168648 1.6306314085734452 chr4 191154276 128634320 0.6729345672602166 3.9734286987639966 chr5 180915260 171223993 0.9464320091074683 2.2378677163252916 chr6 171115067 108907140 0.6364555845920921 3.470849708631605 chr7 159138663 144688030 0.9091947065057345 7.59668089454008 chr8 146364022 150585336 1.028841199786106 2.749726935545966 chr9 141213431 63354627 0.4486444848153289 5.512192761380191 chr10 135534747 140162773 1.03414641708078 14.011788974254875 chr11 135006516 113909364 0.8437323425189344 3.5867260411490016 chr12 133851895 81527130 0.6090846154998403 1.5416283504769661 chr13 115169878 77268323 0.6709073964635093 1.6102105894505159 chr14 107349540 47170258 0.4394081055214582 1.7896037691585291 chr15 102531392 69486153 0.6777061312110149 1.6377967821956556 chr16 90354753 74239634 0.8216461396336283 9.328493889355276 chr17 81195210 75773495 0.9332261718394472 5.764039422205889 chr18 78077248 46787350 0.5992443534895082 6.885577784003345 chr19 59128983 33556345 0.5675109446749659 3.748671699249792 chr20 63025520 44493419 0.7059587766987088 2.1941526292522164 chr21 48129895 20375572 0.4233454488109729 2.4405054321379542 chr22 51304566 27650511 0.538948346234914 1.8451343059552292 chrMT 16571 439616 26.529237825116166 16.4907319385177 chrX 155270560 101230667 0.6519630443787927 2.513212115802036 chrY 59373566 6536520 0.11009141677628054 7.828902673836497