BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549137.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,655,253 number of mapped reads = 9,404,802 (88.26%) number of secondary alignments = 0 number of mapped bases = 373,492,343 bp number of sequenced bases = 373,455,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,622 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2071 >>>>>>> ACTG content number of A's = 106,726,028 bp (28.58%) number of C's = 79,162,700 bp (21.2%) number of T's = 107,734,532 bp (28.85%) number of G's = 79,751,364 bp (21.35%) number of N's = 81,083 bp (0.02%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,199,505 number of insertions = 9,565 mapped reads with insertion percentage = 0.1% number of deletions = 29,086 mapped reads with deletion percentage = 0.31% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.1206X std coverageData = 0.6775X There is a 9.07% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 30821688 0.12365741708623466 1.0614001812785228 chr2 243199373 32016213 0.13164595206419386 0.7078200428534329 chr3 198022430 25517221 0.12886025588111408 0.4556715086263282 chr4 191154276 22897244 0.1197841056927233 0.4483641677792462 chr5 180915260 22760417 0.12580706016728496 0.4618007142587 chr6 171115067 21778812 0.1272758289601698 0.511652039316572 chr7 159138663 21150624 0.13290688511062834 1.105730076933466 chr8 146364022 18938940 0.12939614354134105 0.6453873305462038 chr9 141213431 16204986 0.11475527423450252 0.694490789038184 chr10 135534747 18009071 0.13287419941101894 0.5855578745568759 chr11 135006516 17510449 0.1297007694058263 0.6591907875801479 chr12 133851895 17275558 0.1290647248587702 0.4754300700611158 chr13 115169878 11591951 0.10065089241476838 0.3998256510868997 chr14 107349540 11676113 0.10876723831327083 0.5687830973230183 chr15 102531392 11314275 0.11034937475539199 0.42044347097977575 chr16 90354753 11596456 0.12834361906783143 0.5167655418233986 chr17 81195210 11111575 0.13685012945960728 0.5227157537518206 chr18 78077248 9988563 0.12793180159218726 1.3751049449228743 chr19 59128983 8371912 0.14158728216245492 0.965561823706536 chr20 63025520 8577439 0.13609469624368034 0.4972578523451637 chr21 48129895 4849135 0.10075099893735484 0.49333637575595435 chr22 51304566 4791123 0.09338589863522088 0.4216766802244271 chrMT 16571 103348 6.236678534789693 8.669406533861903 chrX 155270560 12115422 0.07802781158256916 0.45069899322140583 chrY 59373566 2523808 0.04250726661760555 0.3005297764538749