BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008729.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 = 1,886,373 number of mapped reads = 1,641,437 (87.02%) number of supplementary alignments = 13,763 (0.73%) number of secondary alignments = 0 number of mapped bases = 105,772,815 bp number of sequenced bases = 105,689,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,268 duplication rate = 4.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2217 >>>>>>> ACTG content number of A's = 28,522,120 bp (26.99%) number of C's = 19,688,043 bp (18.63%) number of T's = 33,283,761 bp (31.49%) number of G's = 24,118,357 bp (22.82%) number of N's = 77,245 bp (0.07%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 998,314 number of insertions = 8,457 mapped reads with insertion percentage = 0.51% number of deletions = 49,171 mapped reads with deletion percentage = 2.95% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.3294X There is a 2.7% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.11% 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% of reference with a coverageData >= 6X There is a 0% 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 9797532 0.03930795422170683 0.5608463174845686 chr2 243199373 10219498 0.042021070506625034 0.44105522029862415 chr3 198022430 6895659 0.03482261580165439 0.22593731924467775 chr4 191154276 5508494 0.028817006426787962 0.22511386332328967 chr5 180915260 4118447 0.022764508643438923 0.18469047192089094 chr6 171115067 5412460 0.03163052847941204 0.24436180995856796 chr7 159138663 5830208 0.036636024772936544 0.41996151000366394 chr8 146364022 8095380 0.05530990395986795 0.44145719417580725 chr9 141213431 3514950 0.024891045951570996 0.27213770343536264 chr10 135534747 5527405 0.040782198826106196 0.300845620607347 chr11 135006516 4812484 0.03564630910111035 0.3623637924153499 chr12 133851895 4771726 0.03564929730729625 0.23245261007652676 chr13 115169878 2582458 0.022423033217070874 0.18140835231913413 chr14 107349540 3748844 0.03492184503072859 0.22937194203166106 chr15 102531392 2945552 0.028728294257430936 0.21115119169601104 chr16 90354753 3435987 0.03802773939296807 0.2542154751697119 chr17 81195210 2635316 0.03245654515826734 0.27269094756779066 chr18 78077248 1985422 0.025428944421811588 0.435781733636296 chr19 59128983 2662161 0.0450229458538125 0.38482885705610814 chr20 63025520 2656305 0.04214649875161681 0.25616673197482814 chr21 48129895 1439833 0.02991556495188697 0.22443248127186602 chr22 51304566 1298313 0.025305993232649118 0.18812682970120131 chrMT 16571 62584 3.77671836340595 3.237331613496351 chrX 155270560 5475666 0.03526532009673952 0.24413242696153864 chrY 59373566 340131 0.005728660461458555 0.18167547835308406