BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695987.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,302,520 number of mapped reads = 13,911,670 (90.91%) number of supplementary alignments = 20,079 (0.13%) number of secondary alignments = 0 number of mapped bases = 2,075,916,812 bp number of sequenced bases = 2,061,014,162 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,059,826 duplication rate = 19.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.6785 >>>>>>> ACTG content number of A's = 588,574,565 bp (28.56%) number of C's = 442,374,513 bp (21.46%) number of T's = 580,813,798 bp (28.18%) number of G's = 449,251,286 bp (21.8%) number of N's = 0 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0206 number of mismatches = 29,422,157 number of insertions = 12,162,636 mapped reads with insertion percentage = 48.72% number of deletions = 13,339,961 mapped reads with deletion percentage = 54.07% homopolymer indels = 37.87% >>>>>>> Coverage mean coverageData = 0.6706X std coverageData = 2.1281X There is a 21.77% of reference with a coverageData >= 1X There is a 13.01% of reference with a coverageData >= 2X There is a 8.4% of reference with a coverageData >= 3X There is a 5.72% of reference with a coverageData >= 4X There is a 4.05% of reference with a coverageData >= 5X There is a 2.95% of reference with a coverageData >= 6X There is a 2.2% of reference with a coverageData >= 7X There is a 1.67% of reference with a coverageData >= 8X There is a 1.28% of reference with a coverageData >= 9X There is a 1% of reference with a coverageData >= 10X There is a 0.79% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.5% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 188916496 0.757937915027301 2.6052152108363784 chr2 243199373 178748495 0.7349874828830254 2.369536249652531 chr3 198022430 141265348 0.7133805397701665 2.0233939531848364 chr4 191154276 107918920 0.5645645091402507 1.8970373480325042 chr5 180915260 124734033 0.68946109355286 1.9852264203153493 chr6 171115067 114250544 0.6676825483754741 1.9403831627149577 chr7 159138663 103969283 0.6533251005131292 1.937409201621329 chr8 146364022 107837760 0.7367777854587789 2.111752861614172 chr9 141213431 90700456 0.6422934090454895 2.2241845261448066 chr10 135534747 105178413 0.7760254497689807 2.205322729020507 chr11 135006516 109286995 0.8094942247083837 2.3191741940332644 chr12 133851895 96512373 0.7210385254538234 2.0558426806840107 chr13 115169878 58226460 0.5055702151564317 1.6947782492195331 chr14 107349540 64516677 0.6009963060857084 1.8743389422757635 chr15 102531392 69388755 0.6767561977506362 2.0731998390344906 chr16 90354753 72224200 0.7993403512485945 2.600529150243168 chr17 81195210 63286622 0.7794378757072 2.2893783939835766 chr18 78077248 55432599 0.7099712197847957 2.35968801514732 chr19 59128983 35741322 0.6044636688576227 2.055434722860072 chr20 63025520 59591398 0.9455121988680141 2.516015137013485 chr21 48129895 26099741 0.5422771231892362 2.5993389237016715 chr22 51304566 32104006 0.6257533881097445 2.040741761614563 chrMT 16571 176763 10.667008629533523 13.845611047188767 chrX 155270560 59306944 0.38195871773760587 1.3062934070818062 chrY 59373566 10502209 0.1768835814914671 1.1591198886585297