BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819140.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 580,369 number of mapped reads = 506,072 (87.2%) number of supplementary alignments = 3,824 (0.66%) number of secondary alignments = 0 number of mapped bases = 29,073,491 bp number of sequenced bases = 29,065,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,771 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.7424 >>>>>>> ACTG content number of A's = 7,653,629 bp (26.33%) number of C's = 5,330,351 bp (18.34%) number of T's = 8,936,593 bp (30.75%) number of G's = 7,144,300 bp (24.58%) number of N's = 346 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 153,373 number of insertions = 2,627 mapped reads with insertion percentage = 0.52% number of deletions = 4,867 mapped reads with deletion percentage = 0.95% homopolymer indels = 38.83% >>>>>>> Coverage mean coverageData = 0.0094X std coverageData = 0.1512X There is a 0.89% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2813699 0.011288633860615337 0.322121538849178 chr2 243199373 2320673 0.009542265555100753 0.14310213320534287 chr3 198022430 1640330 0.00828355656477905 0.09365116335555594 chr4 191154276 1668954 0.008730926845706553 0.10245821403620617 chr5 180915260 1615981 0.008932253697117644 0.09794831996451987 chr6 171115067 1313256 0.007674695297287877 0.1035739618791545 chr7 159138663 1530706 0.00961869335297859 0.19596201903612784 chr8 146364022 2490050 0.017012719150338737 0.15765567778601364 chr9 141213431 1220312 0.008641614266846898 0.12246278644634423 chr10 135534747 1515811 0.01118392909236773 0.14162825731668602 chr11 135006516 1042705 0.007723367959513895 0.1189287292301273 chr12 133851895 1344824 0.010047104674909534 0.10367409654219711 chr13 115169878 662557 0.005752867082137571 0.07806426815319621 chr14 107349540 709801 0.006612054415882918 0.08573823589580896 chr15 102531392 752310 0.007337362590376224 0.08935007614181377 chr16 90354753 874764 0.009681438673181919 0.1076601577142605 chr17 81195210 958833 0.011808984791097899 0.11548687881083496 chr18 78077248 707559 0.00906229430627473 0.20793610406577065 chr19 59128983 624082 0.01055458707957145 0.2119979202657483 chr20 63025520 750934 0.011914760877815844 0.11319926239139777 chr21 48129895 380144 0.007898292734692232 0.09598324185509154 chr22 51304566 237941 0.004637813328349762 0.06971870255060948 chrMT 16571 18262 1.1020457425623076 1.1976494396662798 chrX 155270560 1762912 0.011353807186629584 0.12072461856415156 chrY 59373566 116091 0.0019552640648196878 0.07697071892140837