BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013365.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 = 1,749,647 number of mapped reads = 1,581,012 (90.36%) number of supplementary alignments = 10,131 (0.58%) number of secondary alignments = 0 number of mapped bases = 107,038,561 bp number of sequenced bases = 106,993,258 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,257 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6488 >>>>>>> ACTG content number of A's = 30,706,723 bp (28.7%) number of C's = 19,427,256 bp (18.16%) number of T's = 34,008,120 bp (31.79%) number of G's = 22,827,701 bp (21.34%) number of N's = 23,458 bp (0.02%) GC percentage = 39.49% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 882,619 number of insertions = 8,508 mapped reads with insertion percentage = 0.53% number of deletions = 26,321 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.402X There is a 3.06% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7863777 0.03154967866659798 0.6497779407684826 chr2 243199373 11830383 0.048644792353144756 0.4731697668210859 chr3 198022430 9091700 0.04591247567257911 0.2334822745551642 chr4 191154276 8324728 0.0435497869793925 0.2463196764906591 chr5 180915260 4946983 0.02734419970985311 0.18220298566883758 chr6 171115067 6750735 0.039451435331524606 0.2861358223239546 chr7 159138663 6480284 0.040720990599248656 0.8121756523821213 chr8 146364022 6923959 0.0473064275317605 0.5826651239078411 chr9 141213431 4429413 0.031366796831103126 0.37462178839621063 chr10 135534747 3753952 0.027697340225233902 0.35508588826671933 chr11 135006516 4047760 0.02998196027812465 0.2758589013708522 chr12 133851895 4812557 0.03595434341814884 0.2174348303190149 chr13 115169878 2427042 0.021073583146454317 0.15759836727123525 chr14 107349540 4034363 0.03758155833737154 0.23847056633451721 chr15 102531392 2109878 0.020577873359994957 0.16263584819913493 chr16 90354753 2402325 0.02658769926580398 0.20885534472331152 chr17 81195210 2832728 0.03488787084853897 0.22146874924780047 chr18 78077248 2841941 0.0363990928573712 0.7405254709342264 chr19 59128983 1419936 0.02401421313131667 0.4547836666649877 chr20 63025520 1673506 0.02655283129754423 0.1883268662608397 chr21 48129895 1606844 0.033385570444315324 0.2214954350223198 chr22 51304566 909379 0.017725108521530034 0.14304529629603527 chrMT 16571 40929 2.4699173254480717 2.159151266253651 chrX 155270560 5275492 0.03397612528736935 0.2331806096107816 chrY 59373566 207967 0.0035026867006775373 0.12524606668458313