BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008801.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 = 1,733,078 number of mapped reads = 1,208,330 (69.72%) number of supplementary alignments = 11,342 (0.65%) number of secondary alignments = 0 number of mapped bases = 78,689,516 bp number of sequenced bases = 78,653,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,789 duplication rate = 10.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7946 >>>>>>> ACTG content number of A's = 21,350,998 bp (27.15%) number of C's = 15,230,000 bp (19.36%) number of T's = 24,166,737 bp (30.73%) number of G's = 17,794,200 bp (22.62%) number of N's = 111,316 bp (0.14%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 650,805 number of insertions = 4,710 mapped reads with insertion percentage = 0.39% number of deletions = 20,532 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.3831X There is a 1.26% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 6945922 0.027867220439141856 0.45349363412915955 chr2 243199373 5735956 0.023585406200862205 0.3503061517785499 chr3 198022430 5791463 0.02924650000507518 0.31596270022793194 chr4 191154276 4855146 0.025399097009998352 0.2845495506237856 chr5 180915260 2640756 0.01459664596563054 0.21202883698582825 chr6 171115067 3548289 0.020736274497674713 0.26166820660856294 chr7 159138663 7403733 0.04652378536069516 0.4192421209028399 chr8 146364022 9052668 0.06185036374581179 0.46838542819540646 chr9 141213431 1805055 0.012782459764751414 0.2145830368888666 chr10 135534747 2874020 0.021205041980858236 0.545635363178107 chr11 135006516 3432141 0.02542203962955388 0.3069075336687675 chr12 133851895 3503219 0.026172352658884658 0.2885466283856809 chr13 115169878 1862578 0.016172440505667636 0.23095476823606248 chr14 107349540 1941950 0.018089970390185183 0.24402308583610766 chr15 102531392 1339483 0.01306412576550214 0.22069046881251234 chr16 90354753 2598422 0.028758000146378575 0.3064097825715709 chr17 81195210 2540102 0.031283889776256506 0.3230312103389254 chr18 78077248 1464605 0.018758409620175137 0.28141783581999774 chr19 59128983 1014436 0.017156324166779598 0.31423492213130166 chr20 63025520 1785020 0.028322178063743066 0.30208043606830526 chr21 48129895 693387 0.014406576203833397 0.20656268204385358 chr22 51304566 639738 0.012469416464803542 0.1942715186216042 chrMT 16571 1160318 70.0210005431175 46.55484776852876 chrX 155270560 3915968 0.02522028644708952 0.29296026707063455 chrY 59373566 145141 0.0024445390394776017 0.07765393849140471