BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472834.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,946,638 number of mapped reads = 2,604,615 (88.39%) number of supplementary alignments = 19,570 (0.66%) number of secondary alignments = 0 number of mapped bases = 170,049,166 bp number of sequenced bases = 169,980,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,856 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5246 >>>>>>> ACTG content number of A's = 45,712,264 bp (26.89%) number of C's = 33,274,543 bp (19.58%) number of T's = 51,261,459 bp (30.16%) number of G's = 39,728,363 bp (23.37%) number of N's = 4,134 bp (0%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,456,288 number of insertions = 13,252 mapped reads with insertion percentage = 0.5% number of deletions = 38,655 mapped reads with deletion percentage = 1.47% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0549X std coverageData = 0.3987X There is a 4.73% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 12460974 0.04999375307474159 0.5378492394404399 chr2 243199373 16399299 0.06743150197184102 0.5914759659256928 chr3 198022430 12270371 0.061964551187458916 0.2785387322153449 chr4 191154276 9337360 0.04884724629440149 0.27912934676366213 chr5 180915260 8643120 0.04777441106958031 0.24710289613986286 chr6 171115067 10475385 0.061218367170437424 0.308517646082711 chr7 159138663 10388003 0.06527642500050412 0.512771794243028 chr8 146364022 9582672 0.06547149954652107 0.4092482100422876 chr9 141213431 9914912 0.07021224489616713 0.48519732322225523 chr10 135534747 7029736 0.051866670028166285 0.37278343429336563 chr11 135006516 5598013 0.041464761597136544 0.36532343859293276 chr12 133851895 7109374 0.05311373440024887 0.26921975893708705 chr13 115169878 6846764 0.059449259814271925 0.28433989492808764 chr14 107349540 3733208 0.03477619000509923 0.24899813823127354 chr15 102531392 3128072 0.030508431993198727 0.2171542310112059 chr16 90354753 5665294 0.06270056429682233 0.3162407895324899 chr17 81195210 3762205 0.046335307218246004 0.26685209322984355 chr18 78077248 2872683 0.03679283112027719 0.7823825763372773 chr19 59128983 3913166 0.066180167516157 0.4175821667911789 chr20 63025520 7395794 0.11734602110383223 0.40885508423397127 chr21 48129895 2068693 0.04298145674325697 0.28454803028104475 chr22 51304566 1966058 0.03832130652854563 0.23116763737456622 chrMT 16571 187796 11.33281033130167 6.737689989423837 chrX 155270560 8417738 0.05421335506228612 0.30446227543149584 chrY 59373566 882476 0.014863112651849142 0.19690634455612857