BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618672.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 221,100,314 number of mapped reads = 213,259,345 (96.45%) number of supplementary alignments = 552,992 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 106,727,095 number of mapped paired reads (second in pair) = 106,532,250 number of mapped paired reads (both in pair) = 210,086,484 number of mapped paired reads (singletons) = 3,172,861 number of mapped bases = 20,658,928,154 bp number of sequenced bases = 20,652,875,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,083,775 duplication rate = 12.04% >>>>>>> Insert size mean insert size = 42,092.275 std insert size = 1,960,380.8728 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.6631 >>>>>>> ACTG content number of A's = 6,112,310,305 bp (29.6%) number of C's = 4,241,629,107 bp (20.54%) number of T's = 6,081,329,204 bp (29.45%) number of G's = 4,214,728,487 bp (20.41%) number of N's = 2,878,441 bp (0.01%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 225,999,332 number of insertions = 2,305,458 mapped reads with insertion percentage = 1.06% number of deletions = 2,631,544 mapped reads with deletion percentage = 1.2% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 6.6734X std coverageData = 62.828X There is a 91.55% of reference with a coverageData >= 1X There is a 89.52% of reference with a coverageData >= 2X There is a 85.39% of reference with a coverageData >= 3X There is a 78.68% of reference with a coverageData >= 4X There is a 69.5% of reference with a coverageData >= 5X There is a 58.57% of reference with a coverageData >= 6X There is a 46.99% of reference with a coverageData >= 7X There is a 35.92% of reference with a coverageData >= 8X There is a 26.2% of reference with a coverageData >= 9X There is a 18.31% of reference with a coverageData >= 10X There is a 12.31% of reference with a coverageData >= 11X There is a 8.02% of reference with a coverageData >= 12X There is a 5.1% of reference with a coverageData >= 13X There is a 3.19% of reference with a coverageData >= 14X There is a 2% of reference with a coverageData >= 15X There is a 1.27% of reference with a coverageData >= 16X There is a 0.84% of reference with a coverageData >= 17X There is a 0.59% of reference with a coverageData >= 18X There is a 0.44% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% 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 0.08% 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 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1688792887 6.7754811611883605 148.3450802320305 chr2 243199373 1792474198 7.370389881720624 38.88218693521636 chr3 198022430 1395185920 7.045595390380776 4.544641104335539 chr4 191154276 1411914135 7.386254519360059 44.24559194594084 chr5 180915260 1273502288 7.039219842483161 6.08492364719947 chr6 171115067 1218774496 7.122543428627474 34.23557940836737 chr7 159138663 1132571697 7.116885838107111 44.48682132161118 chr8 146364022 1069457723 7.306834756153394 98.89389883237786 chr9 141213431 876998874 6.2104494437218225 64.6748168481485 chr10 135534747 1067548439 7.876566435026437 115.54009970000271 chr11 135006516 952833991 7.057688911844818 29.63947517590913 chr12 133851895 925067848 6.911130006788473 5.548143056528104 chr13 115169878 679021775 5.895827857002679 4.212255043468608 chr14 107349540 628330498 5.853127065099674 5.996493043913881 chr15 102531392 596966851 5.8222836865415815 4.677026542803238 chr16 90354753 627364388 6.943346832014471 43.470720035414736 chr17 81195210 558946367 6.883982035393467 35.68265027648845 chr18 78077248 584696506 7.488692557401613 83.81113061327542 chr19 59128983 393375542 6.652837949199972 67.86486498724707 chr20 63025520 426226780 6.762764987896966 13.225287857028135 chr21 48129895 290717276 6.040264081191118 26.431529925610757 chr22 51304566 250242675 4.877590719703194 32.298309208278546 chrMT 16571 5986757 361.27916239213084 48.862390661271256 chrX 155270560 567198233 3.652967008040674 12.69731099239046 chrY 59373566 244732010 4.1219018241215295 68.80781299516717