BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524704.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 = 2,581,502 number of mapped reads = 2,385,087 (92.39%) number of supplementary alignments = 9,172 (0.36%) number of secondary alignments = 0 number of mapped bases = 140,407,273 bp number of sequenced bases = 140,363,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,688 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6485 >>>>>>> ACTG content number of A's = 35,131,207 bp (25.03%) number of C's = 25,138,584 bp (17.91%) number of T's = 43,767,396 bp (31.18%) number of G's = 36,307,630 bp (25.87%) number of N's = 19,099 bp (0.01%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 703,749 number of insertions = 9,836 mapped reads with insertion percentage = 0.41% number of deletions = 27,008 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.0454X std coverageData = 0.4039X There is a 3.86% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% 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 11365637 0.045599232428793025 0.7419888383301668 chr2 243199373 11838503 0.048678180597118564 0.5825185800233527 chr3 198022430 9206383 0.046491617136503176 0.2473674332014998 chr4 191154276 8928500 0.046708345671534965 0.2943989681874242 chr5 180915260 8492911 0.04694413837727122 0.2505218475079845 chr6 171115067 8001454 0.046760663103968515 0.2931170559179589 chr7 159138663 7706181 0.048424316597406626 0.48574615747152605 chr8 146364022 6965358 0.04758927709707239 0.42755932783970896 chr9 141213431 5900709 0.041785749119005546 0.32682371124325477 chr10 135534747 6829890 0.050392169913446624 0.4196046217070509 chr11 135006516 6407341 0.04745949447358526 0.33346971347700644 chr12 133851895 6361153 0.04752381727580323 0.25481795552630115 chr13 115169878 4393319 0.0381464240154878 0.22432315316088122 chr14 107349540 4219694 0.039307983993224375 0.23826164777421865 chr15 102531392 4055048 0.03954933138916128 0.2297025864555533 chr16 90354753 4121034 0.045609487748807194 0.27108566562323405 chr17 81195210 3862236 0.047567288760014294 0.2720812442990814 chr18 78077248 3733496 0.04781797637129833 0.5920737503076243 chr19 59128983 2997140 0.05068817097699786 0.5463457985382649 chr20 63025520 3011998 0.04779013326665135 0.2598953427765122 chr21 48129895 1896843 0.039410910827875276 0.26697322686427644 chr22 51304566 1702501 0.03318420040820538 0.20962522591917004 chrMT 16571 116143 7.008810572687224 4.816724692963562 chrX 155270560 7834494 0.05045704736300301 0.29305834608053777 chrY 59373566 459307 0.0077358836759105895 0.2585370050507353