BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472645.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,587,844 number of mapped reads = 8,530,565 (99.33%) number of supplementary alignments = 43,177 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,271,577 number of mapped paired reads (second in pair) = 4,258,988 number of mapped paired reads (both in pair) = 8,491,818 number of mapped paired reads (singletons) = 38,747 number of mapped bases = 838,624,925 bp number of sequenced bases = 838,496,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,480,643 duplication rate = 42.62% >>>>>>> Insert size mean insert size = 17,957.4604 std insert size = 1,337,754.26 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.5904 >>>>>>> ACTG content number of A's = 226,611,392 bp (27.03%) number of C's = 194,128,393 bp (23.15%) number of T's = 226,350,563 bp (26.99%) number of G's = 191,296,154 bp (22.81%) number of N's = 109,767 bp (0.01%) GC percentage = 45.97% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 6,622,390 number of insertions = 58,895 mapped reads with insertion percentage = 0.68% number of deletions = 56,509 mapped reads with deletion percentage = 0.6% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.2709X std coverageData = 15.1599X There is a 2.11% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.16% 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 0.14% 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 0.13% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 124726223 0.5004048635850741 27.077458079244842 chr2 243199373 61350123 0.2522626692791679 17.76278453825143 chr3 198022430 62521998 0.3157318996640936 12.365005434018512 chr4 191154276 19788945 0.10352342314330441 6.189687522736386 chr5 180915260 24990709 0.13813488701837534 7.425383617745769 chr6 171115067 71974197 0.4206186998132666 16.549728118076125 chr7 159138663 46111977 0.28975973613652894 18.166628219074802 chr8 146364022 38266681 0.2614486844314787 12.750442484238212 chr9 141213431 23521401 0.16656631620259973 10.074437649447077 chr10 135534747 31641632 0.23345771250821754 16.396228990035777 chr11 135006516 50282519 0.37244512701890625 17.12757131118506 chr12 133851895 48838140 0.3648670046845433 14.162578408052594 chr13 115169878 7873643 0.0683654713952202 3.4894374740091734 chr14 107349540 22486765 0.20947239270890217 8.787727328900061 chr15 102531392 11808114 0.11516584111137397 4.729157188560324 chr16 90354753 51092838 0.5654692897007864 21.388510116224506 chr17 81195210 36664228 0.45155653886479263 22.599102928437222 chr18 78077248 12045278 0.15427385452929898 8.086754658029026 chr19 59128983 28663139 0.48475616433314944 15.66081948672932 chr20 63025520 21491242 0.34099269629191475 23.13492960628673 chr21 48129895 8192407 0.1702145205178611 12.907429028263762 chr22 51304566 9566096 0.18645701047349275 7.833898086126551 chrMT 16571 1104 0.06662241264860298 0.3046962947296252 chrX 155270560 23547672 0.15165574208014707 5.341383764207153 chrY 59373566 1177854 0.019838020172141927 1.9215139950934361