BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525127.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 877,726 number of mapped reads = 772,652 (88.03%) number of supplementary alignments = 21,260 (2.42%) number of secondary alignments = 0 number of mapped bases = 58,969,243 bp number of sequenced bases = 58,945,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,505 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4336 >>>>>>> ACTG content number of A's = 14,776,939 bp (25.07%) number of C's = 11,802,703 bp (20.02%) number of T's = 18,389,274 bp (31.2%) number of G's = 13,974,133 bp (23.71%) number of N's = 2,154 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 452,670 number of insertions = 5,443 mapped reads with insertion percentage = 0.69% number of deletions = 13,776 mapped reads with deletion percentage = 1.76% homopolymer indels = 43.29% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.214X There is a 1.77% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 4779833 0.019176814809219674 0.29503076363451664 chr2 243199373 5033903 0.02069866767296312 0.32083945559688903 chr3 198022430 3839639 0.01938991961668181 0.1460548338025708 chr4 191154276 3731872 0.019522827728949154 0.15652965053767134 chr5 180915260 3532286 0.019524533198581478 0.1475377894826244 chr6 171115067 3326365 0.019439346039586334 0.15955088542398912 chr7 159138663 3287878 0.020660460117099263 0.2967055916960013 chr8 146364022 3015402 0.02060207118385965 0.27485510898974297 chr9 141213431 2502545 0.01772172081846804 0.20493592184705337 chr10 135534747 2801386 0.020669135125917195 0.2123799188555847 chr11 135006516 2664655 0.019737232534761506 0.204138985711635 chr12 133851895 2674590 0.01998171187639891 0.14896519331748892 chr13 115169878 1823265 0.015831092570923796 0.1316549546546435 chr14 107349540 1790661 0.016680658342830345 0.15080206849437508 chr15 102531392 1718519 0.016760905772156103 0.13617479818503603 chr16 90354753 1733513 0.019185631551668345 0.153827949864784 chr17 81195210 1704240 0.020989415508624217 0.17277478364273816 chr18 78077248 1575772 0.02018221748799343 0.3348271457315056 chr19 59128983 1293616 0.021877866561648793 0.25004722981440614 chr20 63025520 1256626 0.019938367823065958 0.15048849745829362 chr21 48129895 765905 0.015913290481934357 0.13975275344729005 chr22 51304566 700485 0.013653463124510204 0.1225541773293066 chrMT 16571 1760 0.10620964335284533 0.3358447348690027 chrX 155270560 3256386 0.020972333712198886 0.18460104692499776 chrY 59373566 158141 0.002663491695951023 0.07741280154136927