BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038488.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,623,262 number of mapped reads = 17,975,201 (96.52%) number of supplementary alignments = 260,988 (1.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,089,415 number of mapped paired reads (second in pair) = 8,885,786 number of mapped paired reads (both in pair) = 17,720,318 number of mapped paired reads (singletons) = 254,883 number of mapped bases = 2,421,306,017 bp number of sequenced bases = 2,419,696,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,949,954 duplication rate = 15.89% >>>>>>> Insert size mean insert size = 67,628.3902 std insert size = 2,545,645.632 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 53.4057 >>>>>>> ACTG content number of A's = 691,644,562 bp (28.58%) number of C's = 478,625,405 bp (19.78%) number of T's = 704,720,292 bp (29.12%) number of G's = 544,509,976 bp (22.5%) number of N's = 196,396 bp (0.01%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 29,545,155 number of insertions = 417,712 mapped reads with insertion percentage = 2.21% number of deletions = 831,111 mapped reads with deletion percentage = 4.46% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.7822X std coverageData = 9.9347X There is a 27.24% of reference with a coverageData >= 1X There is a 16.55% of reference with a coverageData >= 2X There is a 9.89% of reference with a coverageData >= 3X There is a 6.45% of reference with a coverageData >= 4X There is a 4.17% of reference with a coverageData >= 5X There is a 2.81% of reference with a coverageData >= 6X There is a 1.91% of reference with a coverageData >= 7X There is a 1.33% of reference with a coverageData >= 8X There is a 0.94% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 210713617 0.84538853365585 13.637481498900144 chr2 243199373 220773163 0.9077867277231837 12.46953549665601 chr3 198022430 169862663 0.8577950639228091 1.9527433858592567 chr4 191154276 105335028 0.5510471970817958 9.918120182254885 chr5 180915260 169484844 0.9368189504854372 2.0010513604156452 chr6 171115067 143051811 0.8359977499818879 8.604612181968749 chr7 159138663 119323887 0.7498107923653977 10.622380808947767 chr8 146364022 155725410 1.0639596252691115 4.484948162977604 chr9 141213431 103264993 0.7312689187475375 18.1000419284077 chr10 135534747 124768198 0.9205624444040169 21.822971449503775 chr11 135006516 110870596 0.821224036327254 7.409837850403832 chr12 133851895 103236350 0.7712729804833918 1.9749030795689086 chr13 115169878 83079018 0.7213606495267799 1.699135389415163 chr14 107349540 78967548 0.7356114241383801 1.848574143099296 chr15 102531392 65104522 0.6349715997223563 1.6262173231752672 chr16 90354753 72209128 0.7991735420935742 8.613297345022028 chr17 81195210 58941894 0.7259282167014532 12.907780765322086 chr18 78077248 96565777 1.2367979081434837 12.554089744856794 chr19 59128983 31450729 0.5319003880043057 6.154909246186385 chr20 63025520 64901285 1.0297619916503664 3.758208674196136 chr21 48129895 23213996 0.4823196892492701 4.7881287751569594 chr22 51304566 13821509 0.2694011484279976 1.049583701177238 chrMT 16571 6713636 405.1436847504677 260.86011438818053 chrX 155270560 85119384 0.5482004057948912 2.280523727415307 chrY 59373566 4807031 0.08096247747692972 10.232518422052493