BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716474.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 = 714,619 number of mapped reads = 635,112 (88.87%) number of supplementary alignments = 3,211 (0.45%) number of secondary alignments = 0 number of mapped bases = 36,909,456 bp number of sequenced bases = 36,899,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,327 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6813 >>>>>>> ACTG content number of A's = 9,464,802 bp (25.65%) number of C's = 6,722,304 bp (18.22%) number of T's = 11,423,607 bp (30.96%) number of G's = 9,288,152 bp (25.17%) number of N's = 274 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 184,731 number of insertions = 2,480 mapped reads with insertion percentage = 0.39% number of deletions = 6,523 mapped reads with deletion percentage = 1.02% homopolymer indels = 41.97% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.1401X There is a 1.11% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4477829 0.017965166875150936 0.20531821212865992 chr2 243199373 3658269 0.015042263287413985 0.18784408944819586 chr3 198022430 2338970 0.011811641741796624 0.11408380250637763 chr4 191154276 1555872 0.008139352320844761 0.10238911625255666 chr5 180915260 2633050 0.01455405143822583 0.1269314767966376 chr6 171115067 1341671 0.007840753146536185 0.09711124237068774 chr7 159138663 2443235 0.015352868711734746 0.19280852204330015 chr8 146364022 1598550 0.01092174140992108 0.125977221017983 chr9 141213431 1014748 0.0071859170392935216 0.10765429677312516 chr10 135534747 1631986 0.012041089359911522 0.130818698448895 chr11 135006516 1598443 0.011839747053394075 0.1378070550943499 chr12 133851895 1502635 0.011226101804535527 0.1117325456441511 chr13 115169878 1051091 0.009126440161723537 0.10024853613738978 chr14 107349540 786066 0.0073224906226892076 0.0912760253879644 chr15 102531392 1617708 0.0157776849455043 0.1329497399400831 chr16 90354753 1073813 0.01188441077360922 0.11778121926105577 chr17 81195210 1409069 0.017354090222809943 0.14303939114862835 chr18 78077248 1187073 0.015203827368505611 0.21329047388904374 chr19 59128983 583525 0.009868679797858184 0.15419325707471462 chr20 63025520 958753 0.015212139463506212 0.1302637634916509 chr21 48129895 456081 0.009476043943166717 0.10660963752777752 chr22 51304566 477011 0.009297632495322151 0.10148087030958788 chrMT 16571 61625 3.718846177056303 2.8830959682748247 chrX 155270560 1363167 0.008779301111556498 0.10505745657099817 chrY 59373566 89216 0.0015026215538409804 0.05439896886704124