BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716441.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,656,359 number of mapped reads = 1,478,524 (89.26%) number of supplementary alignments = 5,512 (0.33%) number of secondary alignments = 0 number of mapped bases = 85,854,092 bp number of sequenced bases = 85,826,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,779 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1873 >>>>>>> ACTG content number of A's = 22,701,376 bp (26.45%) number of C's = 16,696,749 bp (19.45%) number of T's = 25,588,086 bp (29.81%) number of G's = 20,839,896 bp (24.28%) number of N's = 642 bp (0%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 443,405 number of insertions = 7,185 mapped reads with insertion percentage = 0.48% number of deletions = 17,002 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.77% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2332X There is a 2.49% of reference with a coverageData >= 1X There is a 0.21% 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% 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 6871893 0.02757021415806222 0.287259200672411 chr2 243199373 7166386 0.029467123667296626 0.3297618758874288 chr3 198022430 5735586 0.02896432489996209 0.18912000398301582 chr4 191154276 5456092 0.028542871831964668 0.20910883600283467 chr5 180915260 5147203 0.028450905689216044 0.18308213018964561 chr6 171115067 4895480 0.02860928663868039 0.20392191960666486 chr7 159138663 4760359 0.029913277579817293 0.2898763419803043 chr8 146364022 4232564 0.02891806293762548 0.24039190181398074 chr9 141213431 3612236 0.025579974754667636 0.20448777668197876 chr10 135534747 4197309 0.03096850876181589 0.3000589399027971 chr11 135006516 3852077 0.02853252653375634 0.21697039870922624 chr12 133851895 3853766 0.028791269634247614 0.18620983644579153 chr13 115169878 2713214 0.023558364800907405 0.16756495755440817 chr14 107349540 2610236 0.024315297485205806 0.17752024838828195 chr15 102531392 2484363 0.024230266960581205 0.1713914299840939 chr16 90354753 2590329 0.028668430978943633 0.19980753597160408 chr17 81195210 2437066 0.030014898662125512 0.19603500906687937 chr18 78077248 2225888 0.028508791703314135 0.30958757574135914 chr19 59128983 1897935 0.03209821822912124 0.28050176074655025 chr20 63025520 1880492 0.029836993014893013 0.19724697611342543 chr21 48129895 1135786 0.023598347762861314 0.19503676537656073 chr22 51304566 1065198 0.02076224560597589 0.15921210988987694 chrMT 16571 11843 0.7146822762657655 0.9411831424824987 chrX 155270560 4742131 0.03054108261089546 0.20251486917333514 chrY 59373566 278660 0.004693334404067965 0.14863194467597451