BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004090.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 = 1,332,494 number of mapped reads = 1,187,352 (89.11%) number of supplementary alignments = 15,271 (1.15%) number of secondary alignments = 0 number of mapped bases = 78,825,351 bp number of sequenced bases = 78,785,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,382 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6937 >>>>>>> ACTG content number of A's = 22,603,298 bp (28.69%) number of C's = 14,017,243 bp (17.79%) number of T's = 25,591,304 bp (32.48%) number of G's = 16,541,484 bp (21%) number of N's = 31,709 bp (0.04%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 652,873 number of insertions = 5,957 mapped reads with insertion percentage = 0.5% number of deletions = 24,235 mapped reads with deletion percentage = 2.01% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2694X There is a 2.12% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.06% 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 6561500 0.026324909336936014 0.4294254725475358 chr2 243199373 6121594 0.025171092854750082 0.25261850754737825 chr3 198022430 4707168 0.023770882924727264 0.1787982878207165 chr4 191154276 5902707 0.030879283077089 0.20962223429540422 chr5 180915260 4551392 0.025157590354732928 0.18540356570170008 chr6 171115067 4167174 0.02435305127163349 0.19201081536346962 chr7 159138663 6107215 0.03837668913933253 0.34799193888454877 chr8 146364022 4931026 0.0336901509853289 0.5369653069718415 chr9 141213431 2596810 0.01838925647235354 0.2168526195898509 chr10 135534747 2936696 0.02166747690169813 0.24280268045766573 chr11 135006516 4177332 0.030941706546964 0.25152597928357234 chr12 133851895 3903471 0.029162612901371326 0.20265880505942988 chr13 115169878 2557385 0.022205328723192707 0.1721378637333168 chr14 107349540 1818898 0.016943696265489354 0.16141857605847365 chr15 102531392 1748728 0.01705553748846012 0.15072726267969697 chr16 90354753 1862274 0.02061069216801467 0.1842613349166561 chr17 81195210 1524078 0.018770540774511207 0.16901958184547364 chr18 78077248 2408305 0.030845157349808233 0.3909231493028516 chr19 59128983 877998 0.014848860160507073 0.2989085610015917 chr20 63025520 2027513 0.032169714744122696 0.2159323059753084 chr21 48129895 1288781 0.02677714131726238 0.1974665775865461 chr22 51304566 429500 0.008371574569015943 0.10304421762495675 chrMT 16571 3471 0.20946231368052623 0.48462924649731076 chrX 155270560 5424163 0.03493362167303319 0.23760373352110448 chrY 59373566 190172 0.0032029741989894962 0.08125358298309514