BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231842.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,924,768 number of mapped reads = 2,318,317 (59.07%) number of supplementary alignments = 30,052 (0.77%) number of secondary alignments = 0 number of mapped bases = 143,294,591 bp number of sequenced bases = 143,245,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 489,307 duplication rate = 12.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3772 >>>>>>> ACTG content number of A's = 41,779,328 bp (29.17%) number of C's = 28,061,047 bp (19.59%) number of T's = 41,207,554 bp (28.77%) number of G's = 32,187,110 bp (22.47%) number of N's = 10,751 bp (0.01%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 866,955 number of insertions = 9,578 mapped reads with insertion percentage = 0.41% number of deletions = 28,878 mapped reads with deletion percentage = 1.23% homopolymer indels = 44.4% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 5.6141X There is a 1.54% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% 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 14669127 0.058852920571058474 1.2345798943142066 chr2 243199373 9134442 0.03755948005671873 19.900809857798382 chr3 198022430 8203582 0.04142753929441225 0.4771033419671707 chr4 191154276 4993496 0.026122857957935505 0.3929946882427068 chr5 180915260 13295084 0.0734879080957571 0.6319479145011297 chr6 171115067 7372181 0.04308317864259142 0.6468527378951662 chr7 159138663 3974184 0.02497308903493804 0.44742435594062635 chr8 146364022 9310433 0.0636114864348289 0.7425410711966719 chr9 141213431 11171135 0.07910816216907866 0.7239005047725513 chr10 135534747 3895488 0.028741618560737047 0.6547724300049377 chr11 135006516 3318206 0.024578117399903867 0.3770803979775198 chr12 133851895 7191260 0.05372550011339025 0.5433480957710709 chr13 115169878 5376891 0.0466866084550337 0.4986300589552246 chr14 107349540 4100460 0.038197275926846075 0.4893981253692218 chr15 102531392 2785540 0.027167679533698322 0.3701078520580081 chr16 90354753 4950636 0.05479109660119374 0.5600200658270494 chr17 81195210 1821067 0.02242825654370498 0.3394425682667644 chr18 78077248 3019772 0.03867672180248976 0.8359673599871161 chr19 59128983 1537068 0.025995170591721493 0.9424172435044077 chr20 63025520 2776115 0.04404747473721756 0.4821496995421294 chr21 48129895 2420287 0.050286563060235226 0.5309783558518998 chr22 51304566 718223 0.013999202332205675 0.2563154411333927 chrMT 16571 41502 2.504495805926015 3.327501329885665 chrX 155270560 16355221 0.10533368978639608 0.7950680707961174 chrY 59373566 863191 0.01453830480722684 0.31902750785694534