BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124936.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,215,734 number of mapped reads = 4,162,467 (98.74%) number of supplementary alignments = 47,739 (1.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,084,496 number of mapped paired reads (second in pair) = 2,077,971 number of mapped paired reads (both in pair) = 4,147,744 number of mapped paired reads (singletons) = 14,723 number of mapped bases = 563,525,964 bp number of sequenced bases = 563,155,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 628,011 duplication rate = 13.75% >>>>>>> Insert size mean insert size = 59,535.579 std insert size = 2,335,722.5609 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.7377 >>>>>>> ACTG content number of A's = 164,616,478 bp (29.23%) number of C's = 113,560,676 bp (20.17%) number of T's = 165,964,855 bp (29.47%) number of G's = 118,988,309 bp (21.13%) number of N's = 24,994 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 7,753,070 number of insertions = 100,981 mapped reads with insertion percentage = 2.32% number of deletions = 195,858 mapped reads with deletion percentage = 4.54% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.182X std coverageData = 2.4645X There is a 9.72% of reference with a coverageData >= 1X There is a 5.66% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 46563651 0.18681458370368514 3.687378153844214 chr2 243199373 48390652 0.1989752333777604 2.1882498217690527 chr3 198022430 41209619 0.20810581407368853 0.7122681878230196 chr4 191154276 30419098 0.1591337564428849 1.2044557338626989 chr5 180915260 31041411 0.17157983798602727 0.5946036074803476 chr6 171115067 36473485 0.2131518026989406 1.9516935170027985 chr7 159138663 41450824 0.26046985200573164 3.5807392323544884 chr8 146364022 31366063 0.2143017291503509 0.9166911507446875 chr9 141213431 21214018 0.15022663106316 3.2179593373062927 chr10 135534747 25954684 0.19149837642741163 6.907270513242068 chr11 135006516 29157965 0.2159745015566508 2.0428067072493956 chr12 133851895 23086435 0.17247746100270003 0.58995582735185 chr13 115169878 19698371 0.1710375259753249 0.5990360554264731 chr14 107349540 15779235 0.14698931173808477 0.5833364621916686 chr15 102531392 16883855 0.16467010415697858 0.5904753469703282 chr16 90354753 14979408 0.1657843943195772 2.4926652255201804 chr17 81195210 13983897 0.17222563991151696 2.3852897212191673 chr18 78077248 16184069 0.20728277974141712 3.0547764506567487 chr19 59128983 9236046 0.15620167186031256 1.8217898887133652 chr20 63025520 12991233 0.20612655000704477 0.7654904271957778 chr21 48129895 7965271 0.16549529143996677 0.8421535809566033 chr22 51304566 4248477 0.08280894530907834 0.41147766603622987 chrMT 16571 132120 7.972964818055639 5.269149154592649 chrX 155270560 19902347 0.12817849694108144 0.8191325385533309 chrY 59373566 5213730 0.08781231027962848 1.8451615625705697