BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085029.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,824,564 number of mapped reads = 1,658,718 (90.91%) number of supplementary alignments = 11,548 (0.63%) number of secondary alignments = 0 number of mapped bases = 111,086,594 bp number of sequenced bases = 111,048,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,800 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5713 >>>>>>> ACTG content number of A's = 31,035,301 bp (27.95%) number of C's = 21,491,245 bp (19.35%) number of T's = 33,928,336 bp (30.55%) number of G's = 24,588,624 bp (22.14%) number of N's = 5,486 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 942,845 number of insertions = 7,866 mapped reads with insertion percentage = 0.47% number of deletions = 21,900 mapped reads with deletion percentage = 1.31% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.2993X There is a 3.17% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 9453583 0.03792802185235077 0.4434502020998109 chr2 243199373 11268389 0.04633395580341402 0.39359913214429176 chr3 198022430 7322002 0.036975619378067426 0.21059719948354197 chr4 191154276 7731449 0.040446121121559424 0.22602820796961337 chr5 180915260 5637864 0.031163009687518898 0.19377766898819035 chr6 171115067 7794072 0.04554871839544089 0.2821552048979781 chr7 159138663 8596299 0.054017665084945446 0.3373946769236786 chr8 146364022 6679561 0.04563663193130891 0.5233337810390775 chr9 141213431 3365321 0.02383145127321494 0.26776854847616843 chr10 135534747 7031672 0.051880954188079906 0.32870615310268314 chr11 135006516 4544836 0.03366382701113478 0.2759239138049607 chr12 133851895 4779771 0.03570940105106469 0.2136172141312136 chr13 115169878 2191948 0.019032302873499614 0.15115272379012765 chr14 107349540 2742629 0.025548586421516105 0.18932669385311787 chr15 102531392 1903273 0.018562831956870342 0.15229590834189305 chr16 90354753 2631630 0.029125529234748725 0.20029664946931672 chr17 81195210 2788217 0.03433967348566498 0.2303715256316336 chr18 78077248 3236011 0.04144627382358559 0.4414258190712414 chr19 59128983 1490042 0.025199858417994436 0.327286578478545 chr20 63025520 2573459 0.04083201534870319 0.2248291785878848 chr21 48129895 1269674 0.0263801531252042 0.18626173593570766 chr22 51304566 688622 0.013422236141711051 0.12549544608164198 chrMT 16571 6838 0.41264860298111156 0.7019088326090636 chrX 155270560 5137376 0.033086607016809884 0.2204554214003299 chrY 59373566 222056 0.0037399808527586167 0.08194679077456629