BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068112.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,708,753 number of mapped reads = 1,442,779 (84.43%) number of supplementary alignments = 14,063 (0.82%) number of secondary alignments = 0 number of mapped bases = 94,232,142 bp number of sequenced bases = 94,176,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,141 duplication rate = 9.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4544 >>>>>>> ACTG content number of A's = 25,868,367 bp (27.47%) number of C's = 16,319,407 bp (17.33%) number of T's = 31,232,114 bp (33.16%) number of G's = 20,664,614 bp (21.94%) number of N's = 92,479 bp (0.1%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 907,734 number of insertions = 7,193 mapped reads with insertion percentage = 0.5% number of deletions = 34,056 mapped reads with deletion percentage = 2.33% homopolymer indels = 44.84% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.4524X There is a 1.83% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 10604805 0.042546754577594416 1.1360029556255244 chr2 243199373 6874448 0.028266717611973448 0.38555111067360287 chr3 198022430 6190972 0.03126399367990788 0.2722532432414233 chr4 191154276 4653095 0.02434209214341614 0.24209694284605315 chr5 180915260 5009136 0.027687747291190362 0.2627899081966551 chr6 171115067 4987840 0.029149040393970684 0.3437719564646181 chr7 159138663 2218177 0.013938642930536623 0.22877142192344932 chr8 146364022 7248664 0.04952490305301941 0.5099098592339366 chr9 141213431 3095709 0.02192219945424313 0.29953309338047623 chr10 135534747 5499165 0.04057383897282075 0.43123353961318706 chr11 135006516 4249232 0.03147427343432816 0.3005538103350245 chr12 133851895 6794723 0.050762994427535 0.3536117392174463 chr13 115169878 1596664 0.01386355553836742 0.1833250858784802 chr14 107349540 3492199 0.032531103533373316 0.2889220331444235 chr15 102531392 981212 0.009569869099212074 0.1483155609781205 chr16 90354753 2017253 0.022325920142795365 0.24333763774790726 chr17 81195210 2143510 0.026399463712206667 0.24212378464961073 chr18 78077248 2929957 0.03752638668821934 0.5177700093168311 chr19 59128983 3809555 0.06442787964068315 0.7356217197779454 chr20 63025520 597897 0.009486585751295665 0.16630654862296823 chr21 48129895 1060920 0.0220428488364664 0.232851027515732 chr22 51304566 1390264 0.02709825086523488 0.24650586465798643 chrMT 16571 11141 0.6723191117011647 1.1785669126329774 chrX 155270560 6590830 0.042447389897994826 0.335852290220127 chrY 59373566 184774 0.0031120583190169175 0.08450534679456853