BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506338.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,568,509 number of mapped reads = 5,461,398 (83.15%) number of supplementary alignments = 126,554 (1.93%) number of secondary alignments = 0 number of mapped bases = 430,635,951 bp number of sequenced bases = 430,449,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 993,095 duplication rate = 13.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9253 >>>>>>> ACTG content number of A's = 121,185,694 bp (28.15%) number of C's = 77,821,573 bp (18.08%) number of T's = 130,050,224 bp (30.21%) number of G's = 101,286,821 bp (23.53%) number of N's = 105,671 bp (0.02%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 3,114,589 number of insertions = 34,802 mapped reads with insertion percentage = 0.63% number of deletions = 97,894 mapped reads with deletion percentage = 1.76% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.1391X std coverageData = 1.1305X There is a 7.83% of reference with a coverageData >= 1X There is a 3.11% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 33330873 0.13372433282723897 2.1870143218623666 chr2 243199373 33502943 0.1377591668379836 1.0436932267755945 chr3 198022430 26920877 0.13594862460782853 0.5811625743982431 chr4 191154276 25067111 0.13113549706834704 0.7302930977604879 chr5 180915260 33915618 0.18746687261207265 0.6988442542594521 chr6 171115067 16420667 0.09596271846710026 0.5830841875524373 chr7 159138663 22640505 0.1422690411820288 1.295825122207019 chr8 146364022 28960033 0.197863058176961 2.094492394927776 chr9 141213431 12409416 0.08787702353892952 0.9448156285517487 chr10 135534747 25265743 0.18641524449815072 1.201674916441791 chr11 135006516 18615927 0.13788910010832367 0.9474983892842509 chr12 133851895 17857752 0.13341426357841255 0.5914197651741144 chr13 115169878 9620539 0.0835334652347205 0.4507532237100371 chr14 107349540 11552291 0.1076137913585843 0.6011035352739312 chr15 102531392 16073044 0.15676217484689958 0.6386556414307166 chr16 90354753 14488269 0.16034872011658313 0.7300072245631904 chr17 81195210 10546801 0.12989437431099693 0.6667536242520751 chr18 78077248 7879924 0.10092471496946204 1.7466114292930712 chr19 59128983 9453951 0.15988692042952946 1.5541922441632197 chr20 63025520 11129878 0.17659319589905803 0.7073951428173129 chr21 48129895 7452459 0.15484054141402137 0.7556600595805039 chr22 51304566 4656320 0.09075839370710201 0.4842278049912354 chrMT 16571 13835 0.8348922816969404 1.2847138700901855 chrX 155270560 31439236 0.20248034141179114 0.8211628918589277 chrY 59373566 1421939 0.023949024722550772 0.7752641510510261