BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004094.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 = 3,529,195 number of mapped reads = 2,768,266 (78.44%) number of supplementary alignments = 21,789 (0.62%) number of secondary alignments = 0 number of mapped bases = 183,260,915 bp number of sequenced bases = 183,174,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,232 duplication rate = 5.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7468 >>>>>>> ACTG content number of A's = 51,203,441 bp (27.95%) number of C's = 32,981,454 bp (18.01%) number of T's = 59,506,546 bp (32.49%) number of G's = 39,458,883 bp (21.54%) number of N's = 24,235 bp (0.01%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,765,148 number of insertions = 15,979 mapped reads with insertion percentage = 0.57% number of deletions = 52,368 mapped reads with deletion percentage = 1.87% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.0592X std coverageData = 0.4939X There is a 4.11% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.13% 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 15047118 0.060369430333335056 0.7754142237452096 chr2 243199373 17428073 0.07166166912774072 0.6328122459179406 chr3 198022430 11882021 0.06000340971474797 0.335094405481797 chr4 191154276 12004886 0.06280207930059592 0.3581482015076561 chr5 180915260 11820442 0.06533689861209055 0.3489097300333424 chr6 171115067 10889266 0.0636370963171817 0.43084466709299185 chr7 159138663 10744954 0.06751944371934304 0.6381404820272771 chr8 146364022 9610112 0.06565897731342747 0.6962094899272913 chr9 141213431 7270015 0.051482461324801325 0.4477922548065214 chr10 135534747 8830878 0.06515582310416679 0.50158776411619 chr11 135006516 8137616 0.06027572772857867 0.44994839605560916 chr12 133851895 7929300 0.05923935555787238 0.3390677816427783 chr13 115169878 5946957 0.051636392286531725 0.31124327864730805 chr14 107349540 4874524 0.04540796355531659 0.311751827642503 chr15 102531392 5236903 0.05107609384645826 0.3123842273070542 chr16 90354753 4997927 0.055314489100534645 0.34121210317611306 chr17 81195210 4461160 0.05494363522183143 0.3653611002566208 chr18 78077248 4958825 0.06351178002585336 0.8356017744652561 chr19 59128983 2869905 0.04853634976268745 0.5700046972527131 chr20 63025520 3527199 0.05596461560333021 0.33118008185460146 chr21 48129895 2452573 0.05095737275138456 0.33161668950639966 chr22 51304566 1676014 0.03266793056976644 0.23880633100119975 chrMT 16571 78822 4.756623016112486 4.145252289434716 chrX 155270560 9978894 0.06426777877274352 0.3748156553336763 chrY 59373566 606531 0.010215505667960048 0.17739408198264497