BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716206.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 = 1,333,061 number of mapped reads = 1,118,779 (83.93%) number of supplementary alignments = 24,889 (1.87%) number of secondary alignments = 0 number of mapped bases = 83,919,457 bp number of sequenced bases = 83,890,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,627 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1032 >>>>>>> ACTG content number of A's = 21,252,234 bp (25.33%) number of C's = 17,927,122 bp (21.37%) number of T's = 25,105,442 bp (29.93%) number of G's = 19,594,910 bp (23.36%) number of N's = 10,408 bp (0.01%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 631,925 number of insertions = 7,136 mapped reads with insertion percentage = 0.63% number of deletions = 17,338 mapped reads with deletion percentage = 1.53% homopolymer indels = 40.59% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2367X There is a 2.43% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 6814932 0.027341685138670125 0.2576530908559782 chr2 243199373 7227219 0.02971726000296884 0.3271657066158112 chr3 198022430 5627168 0.028416821266156567 0.18228984994416308 chr4 191154276 5300005 0.027726321957872394 0.1908648400994906 chr5 180915260 5028144 0.027792813055128682 0.1817259315615533 chr6 171115067 4824437 0.028194109873445568 0.19768898631519613 chr7 159138663 4555261 0.02862447700719969 0.29686688629139096 chr8 146364022 4280957 0.02924869747020207 0.30145315244370735 chr9 141213431 3639382 0.025772208593954495 0.2389559103044087 chr10 135534747 3830689 0.02826351975999188 0.23871331410768346 chr11 135006516 3810734 0.028226296869997 0.2543063886122152 chr12 133851895 3886734 0.029037571713123673 0.18624781340041796 chr13 115169878 2709068 0.02352236580471154 0.1668227342364693 chr14 107349540 2494979 0.023241636619961297 0.1891865748061012 chr15 102531392 2485910 0.024245355022586644 0.17031980634462995 chr16 90354753 2462088 0.02724912545552529 0.19344534942947972 chr17 81195210 2304129 0.028377646907988784 0.19655943567905648 chr18 78077248 2264747 0.029006491109932562 0.44229523760411166 chr19 59128983 1689927 0.028580349504742877 0.24013220173215255 chr20 63025520 1768149 0.028054492846707173 0.1878404758587443 chr21 48129895 1105504 0.022969175395042934 0.17639682385799665 chr22 51304566 962718 0.01876476257493339 0.15024696614602662 chrMT 16571 6383 0.3851909963188703 0.7316906805302424 chrX 155270560 4626575 0.029796859108384744 0.2174038311536429 chrY 59373566 213618 0.0035978637361953297 0.11003488918483867