BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708551.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,165,495 number of mapped reads = 4,259,015 (82.45%) number of supplementary alignments = 137 (0%) number of secondary alignments = 0 number of mapped bases = 212,380,233 bp number of sequenced bases = 212,361,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,537 duplication rate = 0.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0189 >>>>>>> ACTG content number of A's = 65,975,510 bp (31.07%) number of C's = 40,116,105 bp (18.89%) number of T's = 65,703,744 bp (30.94%) number of G's = 40,557,996 bp (19.1%) number of N's = 7,666 bp (0%) GC percentage = 37.99% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 333,303 number of insertions = 14,336 mapped reads with insertion percentage = 0.34% number of deletions = 11,325 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.0686X std coverageData = 0.2748X There is a 6.33% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% 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 17646305 0.0707974364485134 0.2802459685873705 chr2 243199373 19518252 0.08025617730519395 0.2962369535169236 chr3 198022430 20447580 0.10325890859939452 0.33564626258154207 chr4 191154276 16731046 0.08752640197282326 0.30828514091571496 chr5 180915260 12341336 0.06821611399723826 0.27145741170493703 chr6 171115067 14228182 0.08314979066104097 0.30129512259951363 chr7 159138663 12994961 0.08165810089783147 0.2980900908400025 chr8 146364022 10073701 0.06882634722896587 0.27366524165952305 chr9 141213431 8183789 0.057953333065039685 0.2524383543417371 chr10 135534747 8689606 0.06411349260865186 0.26413923391685445 chr11 135006516 8779214 0.06502807612634046 0.2675604989929992 chr12 133851895 8676988 0.06482529066921316 0.26596780173129575 chr13 115169878 8708604 0.07561529239442279 0.2878164610970571 chr14 107349540 5519572 0.05141682023043601 0.2391548528439756 chr15 102531392 5123717 0.04997217827687349 0.2339262539413576 chr16 90354753 2772312 0.03068252535646907 0.18117522650147128 chr17 81195210 2427904 0.029902059493411 0.1790373457432817 chr18 78077248 6986853 0.08948641478757038 0.31265573920882517 chr19 59128983 1223603 0.020693794107705183 0.14773561447963 chr20 63025520 2522863 0.040029229429602485 0.20891677311920853 chr21 48129895 2353144 0.04889152573468112 0.2324810392042739 chr22 51304566 876990 0.017093800189246312 0.1351115102500278 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 15221551 0.09803243448081851 0.3291333418267986 chrY 59373566 332060 0.005592724546812634 0.0785548977959689