BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525241.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 = 1,582,064 number of mapped reads = 1,456,679 (92.07%) number of supplementary alignments = 5,413 (0.34%) number of secondary alignments = 0 number of mapped bases = 84,839,631 bp number of sequenced bases = 84,811,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,960 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.002 >>>>>>> ACTG content number of A's = 20,433,110 bp (24.09%) number of C's = 16,921,453 bp (19.95%) number of T's = 27,676,194 bp (32.63%) number of G's = 19,779,431 bp (23.32%) number of N's = 1,801 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 417,348 number of insertions = 5,275 mapped reads with insertion percentage = 0.36% number of deletions = 17,092 mapped reads with deletion percentage = 1.17% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.2677X There is a 2.49% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 8814840 0.03536536825719684 0.47310285790694406 chr2 243199373 6706842 0.027577546427309252 0.34148126243287336 chr3 198022430 9029428 0.045598006246060106 0.23254824936247206 chr4 191154276 4593081 0.024028136310170745 0.17532278426071132 chr5 180915260 3530471 0.019514500877372092 0.15095848533316678 chr6 171115067 5126775 0.029960979415097327 0.20947056473004672 chr7 159138663 5964828 0.037481953709765675 0.4643923285180325 chr8 146364022 4630593 0.03163750856750848 0.2612321190233678 chr9 141213431 2681251 0.018987223672796393 0.1850990064330825 chr10 135534747 4327862 0.03193175252689998 0.2730741138001909 chr11 135006516 3627737 0.02687082896058143 0.2182003943568961 chr12 133851895 3155227 0.023572523945215716 0.16901989350370789 chr13 115169878 2488512 0.021607316454741753 0.16225934679406845 chr14 107349540 2985137 0.027807636623314827 0.18263834538619023 chr15 102531392 2162970 0.02109568550478667 0.16166085476574338 chr16 90354753 2160832 0.023914978772616422 0.1828600368481056 chr17 81195210 1570113 0.019337507717511908 0.15519640767975035 chr18 78077248 1706122 0.02185171792940243 0.3319443632472216 chr19 59128983 1500981 0.025384860754327537 0.3148016768670068 chr20 63025520 1450109 0.023008282993936424 0.1662440710803918 chr21 48129895 1054369 0.021906738005557667 0.16883897355295144 chr22 51304566 687944 0.013409020943671954 0.12382508422022964 chrMT 16571 21127 1.2749381449520247 1.4657420256577414 chrX 155270560 4612811 0.029708213842984787 0.20042417803315501 chrY 59373566 249669 0.004205053137620199 0.11989242962918524