BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671993.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 32,272,412 number of mapped reads = 32,171,747 (99.69%) number of supplementary alignments = 201,808 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,094,151 number of mapped paired reads (second in pair) = 16,077,596 number of mapped paired reads (both in pair) = 32,117,074 number of mapped paired reads (singletons) = 54,673 number of mapped bases = 4,444,994,327 bp number of sequenced bases = 4,443,437,866 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,464,331 duplication rate = 57.39% >>>>>>> Insert size mean insert size = 38,448.8209 std insert size = 1,859,329.1512 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 52.9695 >>>>>>> ACTG content number of A's = 1,047,058,622 bp (23.56%) number of C's = 1,106,968,790 bp (24.91%) number of T's = 1,074,936,434 bp (24.19%) number of G's = 1,214,461,535 bp (27.33%) number of N's = 12,485 bp (0%) GC percentage = 52.24% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 35,665,172 number of insertions = 359,217 mapped reads with insertion percentage = 1.08% number of deletions = 890,544 mapped reads with deletion percentage = 2.7% homopolymer indels = 43.79% >>>>>>> Coverage mean coverageData = 1.4359X std coverageData = 97.5732X There is a 4.82% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 547032786 2.1947098218062213 128.49076866176557 chr2 243199373 359886882 1.4798018496536174 89.93567034572435 chr3 198022430 19456053 0.09825176370171804 3.3501383158829903 chr4 191154276 223442776 1.168913302258538 77.4282406473767 chr5 180915260 118933125 0.6573968663561051 54.8870497552771 chr6 171115067 199071732 1.1633793300037103 71.46576603183317 chr7 159138663 153350019 0.9636251562575966 66.41633058508117 chr8 146364022 13883783 0.0948578947905654 2.43225274950089 chr9 141213431 234974285 1.6639655543812968 109.88785574782105 chr10 135534747 194196925 1.4328202125171636 77.84733420083512 chr11 135006516 314567994 2.3300208265503275 118.38917063846492 chr12 133851895 238277705 1.7801593694284268 121.09760056171635 chr13 115169878 123445864 1.0718589456177074 94.24998937908423 chr14 107349540 107206007 0.9986629379129152 66.2087974039041 chr15 102531392 100991710 0.9849833112574927 54.911206639439996 chr16 90354753 377717221 4.180380206451342 200.11204613101705 chr17 81195210 491286191 6.0506794797377825 242.9756507416255 chr18 78077248 8785220 0.11251959085443175 10.778076609028705 chr19 59128983 79187283 1.339229578834461 108.06883205279924 chr20 63025520 81153731 1.2876328668133163 77.18544855613911 chr21 48129895 50309645 1.0452888999653958 86.4266878055952 chr22 51304566 8502821 0.1657322469115127 10.215842033995083 chrMT 16571 43554 2.62832659465331 9.33166239009655 chrX 155270560 393067176 2.5314984115469152 115.33967038656266 chrY 59373566 6223839 0.10482508327022164 15.64394347187336