BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504717.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,051,590 number of mapped reads = 1,834,675 (89.43%) number of secondary alignments = 0 number of mapped bases = 58,703,752 bp number of sequenced bases = 58,703,752 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 414,231 duplication rate = 14.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 6.6514 >>>>>>> ACTG content number of A's = 16,925,823 bp (28.83%) number of C's = 11,529,366 bp (19.64%) number of T's = 18,692,238 bp (31.84%) number of G's = 11,556,223 bp (19.69%) number of N's = 102 bp (0%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 33,027 >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.7312X There is a 0.77% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 5485822 0.022009261112332396 1.1431385952640762 chr2 243199373 5039320 0.020720941579072245 0.7852144075511146 chr3 198022430 3085356 0.015580841018868419 0.32055410332613965 chr4 191154276 4368954 0.022855643574512557 0.7978312708271366 chr5 180915260 3345160 0.018490203645618396 0.522637383283281 chr6 171115067 3357914 0.01962371904982511 0.4127118258599909 chr7 159138663 2875170 0.01806707399571404 0.41120963679526884 chr8 146364022 670384 0.004580251286070835 0.11860031666742908 chr9 141213431 3040992 0.021534722146932327 1.0800451145197216 chr10 135534747 1907260 0.014072110969447561 0.4944612444363262 chr11 135006516 2961494 0.021935933818186967 0.6023877943516555 chr12 133851895 2989078 0.0223312340852552 0.8513370035994612 chr13 115169878 1952428 0.01695259241309607 0.3909422934267453 chr14 107349540 2237282 0.02084109536007327 0.8324090735096481 chr15 102531392 2566424 0.02503061696460729 1.3324042035801371 chr16 90354753 1208396 0.013373906295776162 0.7281495143781624 chr17 81195210 1394742 0.01717763892722243 0.437348254127985 chr18 78077248 1198318 0.01534785139968048 0.43208763079310375 chr19 59128983 973656 0.016466645468940333 0.6368536257735916 chr20 63025520 968958 0.015374058000632124 0.367872639166828 chr21 48129895 1262198 0.026224823469903683 1.3201722658624842 chr22 51304566 224162 0.004369240741652507 0.09276553371583496 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 5353236 0.034476825484496224 0.86488095536563 chrY 59373566 237016 0.003991944832823415 0.1366115419357194