BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003998.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 = 3,476,070 number of mapped reads = 3,104,368 (89.31%) number of supplementary alignments = 26,606 (0.77%) number of secondary alignments = 0 number of mapped bases = 200,044,754 bp number of sequenced bases = 199,963,546 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,426 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5337 >>>>>>> ACTG content number of A's = 54,901,717 bp (27.46%) number of C's = 38,868,110 bp (19.44%) number of T's = 59,989,061 bp (30%) number of G's = 46,176,236 bp (23.09%) number of N's = 28,422 bp (0.01%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,729,452 number of insertions = 17,069 mapped reads with insertion percentage = 0.54% number of deletions = 49,331 mapped reads with deletion percentage = 1.57% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0646X std coverageData = 0.6029X There is a 5.49% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 17137202 0.06875490191857937 1.0849227015208711 chr2 243199373 16879824 0.06940734999345578 0.8530854440838194 chr3 198022430 10243176 0.051727352300443945 0.2592659902998941 chr4 191154276 12331874 0.06451267666123252 0.32033992797573035 chr5 180915260 7884969 0.04358376955045141 0.24292367569316697 chr6 171115067 11569382 0.06761170832490163 0.3796488660775184 chr7 159138663 13522245 0.08497146290590615 1.0731970206151296 chr8 146364022 13190431 0.0901207196943522 0.5341650016048387 chr9 141213431 7700438 0.054530492924571745 0.5754628849159148 chr10 135534747 9661871 0.071287040510726 0.5242571694599324 chr11 135006516 9967250 0.07382791805397007 0.5337546912411651 chr12 133851895 8199602 0.06125876663905281 0.2929688580052562 chr13 115169878 6625228 0.057525701294916715 0.27129817291199465 chr14 107349540 5794165 0.05397475387412 0.34819353826546223 chr15 102531392 6262552 0.06107936191873802 0.3035766643889136 chr16 90354753 6591195 0.07294796102203943 0.3720898842963809 chr17 81195210 5892104 0.07256713788904542 0.3616843442143832 chr18 78077248 6147000 0.07872972162133583 1.1158854649565877 chr19 59128983 4431875 0.07495266745920524 0.7980418568637255 chr20 63025520 5260969 0.0834736309989985 0.3606158390600199 chr21 48129895 2580065 0.053606287734473554 0.3095146015076539 chr22 51304566 2386032 0.04650720561596798 0.2433872293024101 chrMT 16571 64874 3.9149115925411864 4.105566793226448 chrX 155270560 9178904 0.059115546437135284 0.3541108878382232 chrY 59373566 541527 0.009120675015544796 0.1877574283868726