BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716285.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 = 1,049,841 number of mapped reads = 960,814 (91.52%) number of supplementary alignments = 4,330 (0.41%) number of secondary alignments = 0 number of mapped bases = 55,516,247 bp number of sequenced bases = 55,502,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,179 duplication rate = 1.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0584 >>>>>>> ACTG content number of A's = 14,304,585 bp (25.77%) number of C's = 11,330,241 bp (20.41%) number of T's = 16,833,313 bp (30.33%) number of G's = 13,032,781 bp (23.48%) number of N's = 1,218 bp (0%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 264,979 number of insertions = 4,141 mapped reads with insertion percentage = 0.43% number of deletions = 8,452 mapped reads with deletion percentage = 0.87% homopolymer indels = 39.34% >>>>>>> Coverage mean coverageData = 0.0179X std coverageData = 0.1655X There is a 1.67% of reference with a coverageData >= 1X There is a 0.09% 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 4298516 0.017245758436846583 0.23439546978050058 chr2 243199373 4788753 0.019690646982054513 0.18183345567126105 chr3 198022430 3631398 0.018338316523032264 0.14291398462860802 chr4 191154276 3623940 0.018958194793403417 0.152601833360725 chr5 180915260 3440841 0.019019075560569074 0.14626073779529492 chr6 171115067 3259484 0.01904849208865985 0.1512904165932115 chr7 159138663 2965036 0.018631776490418295 0.17427076116033388 chr8 146364022 2833851 0.019361663893056998 0.15860260198802098 chr9 141213431 2348974 0.016634210948390595 0.16477119424257713 chr10 135534747 2597310 0.01916342530229536 0.17067230454556168 chr11 135006516 2519749 0.018663906562850642 0.16198033352471994 chr12 133851895 2511453 0.018762924499499987 0.14547516457064857 chr13 115169878 1737042 0.015082433273047315 0.12913984959209077 chr14 107349540 1672975 0.015584370459342443 0.1365976352035375 chr15 102531392 1587581 0.015483852984264565 0.13088494428536068 chr16 90354753 1583067 0.017520572492738706 0.14703360822915956 chr17 81195210 1554871 0.019149787284249896 0.15123356589170503 chr18 78077248 1461872 0.018723405824959405 0.25236729926302326 chr19 59128983 1097270 0.018557227679698127 0.18485921107395373 chr20 63025520 1148135 0.018216985754342052 0.1465130449301526 chr21 48129895 679066 0.01410902724803368 0.13286534793879617 chr22 51304566 688449 0.013418864122152402 0.12185420880049568 chrMT 16571 2853 0.17216824573049302 0.4193298787552338 chrX 155270560 3322448 0.021397797496189877 0.16603246900406515 chrY 59373566 161313 0.002716916144130538 0.07283131520704918