BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173852.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 = 7,157,506 number of mapped reads = 6,951,462 (97.12%) number of supplementary alignments = 728,728 (10.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,481,359 number of mapped paired reads (second in pair) = 3,470,103 number of mapped paired reads (both in pair) = 6,816,476 number of mapped paired reads (singletons) = 134,986 number of mapped bases = 815,584,118 bp number of sequenced bases = 815,047,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,285,096 duplication rate = 63.87% >>>>>>> Insert size mean insert size = 859,401.2921 std insert size = 8,362,981.9948 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.6567 >>>>>>> ACTG content number of A's = 245,092,266 bp (30.07%) number of C's = 160,014,666 bp (19.63%) number of T's = 244,469,228 bp (29.99%) number of G's = 165,462,772 bp (20.3%) number of N's = 8,996 bp (0%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 8,528,935 number of insertions = 86,523 mapped reads with insertion percentage = 1.2% number of deletions = 216,847 mapped reads with deletion percentage = 3.04% homopolymer indels = 41.68% >>>>>>> Coverage mean coverageData = 0.2635X std coverageData = 3.8309X There is a 5.74% of reference with a coverageData >= 1X There is a 4.48% of reference with a coverageData >= 2X There is a 3.39% of reference with a coverageData >= 3X There is a 2.75% of reference with a coverageData >= 4X There is a 2.05% of reference with a coverageData >= 5X There is a 1.65% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.71% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 63436409 0.25450852938897994 2.638049175201631 chr2 243199373 69162592 0.28438639107840136 11.821780949033423 chr3 198022430 68086547 0.34383249917698716 1.6740265072755287 chr4 191154276 40497824 0.21185936745668196 1.7183403890008013 chr5 180915260 52189938 0.28847725725292606 1.497278698174666 chr6 171115067 43883210 0.2564543892560905 1.689980551359125 chr7 159138663 46891078 0.2946554728815335 2.399214340548207 chr8 146364022 48280346 0.3298648488902553 2.7299658646609646 chr9 141213431 33943601 0.24037091061118684 1.750226449267609 chr10 135534747 40924643 0.3019494550722111 3.4506393418090586 chr11 135006516 31009246 0.22968703229109327 1.4061282170514033 chr12 133851895 35925519 0.26839753744240974 1.462669570356307 chr13 115169878 20437642 0.1774564873638227 1.1815011867953042 chr14 107349540 24661236 0.2297283807643703 1.3550330302383602 chr15 102531392 27090744 0.2642190208438797 1.4400810065095606 chr16 90354753 25680926 0.28422329924359374 2.0977857370174195 chr17 81195210 33147083 0.4082393899837195 2.026610586154528 chr18 78077248 15618860 0.2000436798182231 2.633283029311886 chr19 59128983 12654268 0.21401125738962903 2.009154599734691 chr20 63025520 35672244 0.5659968216049626 2.3921216013495283 chr21 48129895 10282161 0.21363356392113467 1.42946492438249 chr22 51304566 6057971 0.11807859362848913 0.9306368564440496 chrMT 16571 1519475 91.69482831452538 65.59454447983869 chrX 155270560 26929649 0.17343692841708047 1.1701304432521766 chrY 59373566 1600906 0.026963278574172217 1.041103070335247