BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,018,980 number of mapped reads = 2,955,939 (97.91%) number of supplementary alignments = 274,771 (9.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,478,882 number of mapped paired reads (second in pair) = 1,477,057 number of mapped paired reads (both in pair) = 2,913,534 number of mapped paired reads (singletons) = 42,405 number of mapped bases = 350,843,193 bp number of sequenced bases = 350,666,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,258,123 duplication rate = 65.14% >>>>>>> Insert size mean insert size = 961,313.016 std insert size = 9,262,986.5051 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.9262 >>>>>>> ACTG content number of A's = 105,736,809 bp (30.15%) number of C's = 68,449,997 bp (19.52%) number of T's = 105,638,297 bp (30.12%) number of G's = 70,837,139 bp (20.2%) number of N's = 4,395 bp (0%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 3,251,893 number of insertions = 36,054 mapped reads with insertion percentage = 1.18% number of deletions = 72,041 mapped reads with deletion percentage = 2.38% homopolymer indels = 43.54% >>>>>>> Coverage mean coverageData = 0.1133X std coverageData = 1.768X There is a 2.49% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 1.46% of reference with a coverageData >= 3X There is a 1.18% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.52% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 30115140 0.12082272806052508 1.1622923055913403 chr2 243199373 34547720 0.14205513597273953 5.0443565246483235 chr3 198022430 26030406 0.13145180573736015 1.040968197359653 chr4 191154276 24734164 0.12939372593475232 1.0931427601119161 chr5 180915260 24050282 0.13293672407733875 1.0546759820646094 chr6 171115067 19679297 0.11500621976205053 0.9777327978729431 chr7 159138663 25563804 0.16063854953965523 1.6030509320953366 chr8 146364022 14016571 0.09576513960514149 0.962485846102762 chr9 141213431 13181713 0.09334602882072882 0.9513024549446222 chr10 135534747 12126542 0.08947183116075762 1.5099777662882616 chr11 135006516 16724658 0.12388037626272794 0.9988662319951642 chr12 133851895 13087514 0.09777608303565669 0.8856411428307616 chr13 115169878 11534271 0.10015006701665517 0.9147949869654827 chr14 107349540 8162931 0.0760406705049691 0.7789986523411901 chr15 102531392 10669940 0.1040651042755764 0.9064308655184192 chr16 90354753 13667353 0.1512632434510667 1.3746336185651484 chr17 81195210 7960614 0.09804290179186678 0.9353492860939809 chr18 78077248 6547746 0.08386240765043358 1.1849357400428457 chr19 59128983 6379961 0.10789904842435731 1.3457154726492837 chr20 63025520 10651485 0.16900273095723764 1.1614523057848571 chr21 48129895 5315768 0.11044628291834005 0.9625147284752039 chr22 51304566 3001836 0.05851011389512582 0.6578566699085109 chrMT 16571 1271910 76.75517470279404 63.96823087298065 chrX 155270560 11347087 0.0730794491885648 0.767919851044634 chrY 59373566 474480 0.007991435111039145 0.3550156687286192