BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354864.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 245,911,020 number of mapped reads = 240,636,165 (97.85%) number of supplementary alignments = 7,812,750 (3.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 120,457,903 number of mapped paired reads (second in pair) = 120,178,262 number of mapped paired reads (both in pair) = 240,127,586 number of mapped paired reads (singletons) = 508,579 number of mapped bases = 29,456,310,482 bp number of sequenced bases = 29,442,336,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 200,101,403 duplication rate = 82.57% >>>>>>> Insert size mean insert size = 302,238.3632 std insert size = 6,429,869.9448 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 53.705 >>>>>>> ACTG content number of A's = 8,205,212,455 bp (27.87%) number of C's = 6,324,356,929 bp (21.48%) number of T's = 8,274,159,721 bp (28.1%) number of G's = 6,637,972,785 bp (22.55%) number of N's = 634,439 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 177,470,779 number of insertions = 4,882,143 mapped reads with insertion percentage = 1.9% number of deletions = 5,219,139 mapped reads with deletion percentage = 2.08% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 9.5153X std coverageData = 385.1501X There is a 73.47% of reference with a coverageData >= 1X There is a 70.92% of reference with a coverageData >= 2X There is a 65.09% of reference with a coverageData >= 3X There is a 62.3% of reference with a coverageData >= 4X There is a 56.3% of reference with a coverageData >= 5X There is a 53.65% of reference with a coverageData >= 6X There is a 47.94% of reference with a coverageData >= 7X There is a 45.51% of reference with a coverageData >= 8X There is a 40.32% of reference with a coverageData >= 9X There is a 38.13% of reference with a coverageData >= 10X There is a 33.57% of reference with a coverageData >= 11X There is a 31.61% of reference with a coverageData >= 12X There is a 27.66% of reference with a coverageData >= 13X There is a 25.94% of reference with a coverageData >= 14X There is a 22.59% of reference with a coverageData >= 15X There is a 21.11% of reference with a coverageData >= 16X There is a 18.3% of reference with a coverageData >= 17X There is a 17.03% of reference with a coverageData >= 18X There is a 14.71% of reference with a coverageData >= 19X There is a 13.64% of reference with a coverageData >= 20X There is a 11.74% of reference with a coverageData >= 21X There is a 10.86% of reference with a coverageData >= 22X There is a 9.32% of reference with a coverageData >= 23X There is a 8.59% of reference with a coverageData >= 24X There is a 7.35% of reference with a coverageData >= 25X There is a 6.76% of reference with a coverageData >= 26X There is a 5.77% of reference with a coverageData >= 27X There is a 5.29% of reference with a coverageData >= 28X There is a 4.51% of reference with a coverageData >= 29X There is a 4.13% of reference with a coverageData >= 30X There is a 3.52% of reference with a coverageData >= 31X There is a 3.21% of reference with a coverageData >= 32X There is a 2.73% of reference with a coverageData >= 33X There is a 2.5% of reference with a coverageData >= 34X There is a 2.12% of reference with a coverageData >= 35X There is a 1.93% of reference with a coverageData >= 36X There is a 1.65% of reference with a coverageData >= 37X There is a 1.5% of reference with a coverageData >= 38X There is a 1.28% of reference with a coverageData >= 39X There is a 1.17% of reference with a coverageData >= 40X There is a 1% of reference with a coverageData >= 41X There is a 0.91% of reference with a coverageData >= 42X There is a 0.78% of reference with a coverageData >= 43X There is a 0.71% of reference with a coverageData >= 44X There is a 0.62% of reference with a coverageData >= 45X There is a 0.56% of reference with a coverageData >= 46X There is a 0.49% of reference with a coverageData >= 47X There is a 0.45% of reference with a coverageData >= 48X There is a 0.39% of reference with a coverageData >= 49X There is a 0.36% of reference with a coverageData >= 50X There is a 0.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2392650846 9.59937767216235 247.367922290331 chr2 243199373 2560465106 10.528255375066284 1301.9511082946356 chr3 198022430 2003520322 10.117643349796284 21.685033527490887 chr4 191154276 1980578764 10.361153333551377 122.22161925188115 chr5 180915260 1807411520 9.990376267872595 12.058112709014097 chr6 171115067 1766537280 10.323680497404709 36.9478710703201 chr7 159138663 1561669454 9.813262374838477 170.53890501208699 chr8 146364022 1446724548 9.884427390222989 32.440368117204905 chr9 141213431 1321999989 9.361715664284086 119.49026842952652 chr10 135534747 1562190479 11.526125318992921 316.2543738690755 chr11 135006516 1400163735 10.37108264463324 49.60259221809552 chr12 133851895 1237127046 9.242506772130495 11.779027166502633 chr13 115169878 963086103 8.362308962418107 10.277811791081213 chr14 107349540 932018577 8.682091949346033 53.47159486132579 chr15 102531392 861787989 8.405113518794321 10.173409094014035 chr16 90354753 863303527 9.554600044117214 60.72863345880177 chr17 81195210 731131280 9.004610986288476 56.30088564949699 chr18 78077248 847770885 10.85810407918066 126.02542176755468 chr19 59128983 587468472 9.935372505899519 119.85339000364051 chr20 63025520 577707707 9.16625054422399 41.11011267431653 chr21 48129895 418748944 8.700391804303749 70.13378042416386 chr22 51304566 357547454 6.969115653370891 30.20015011159792 chrMT 16571 207956900 12549.447830547342 2547.5664804042226 chrX 155270560 712906411 4.591381721042289 21.879615260285604 chrY 59373566 353837144 5.959506356751421 165.00074411548508