BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504720.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 = 1,975,987 number of mapped reads = 1,757,870 (88.96%) number of secondary alignments = 0 number of mapped bases = 56,246,196 bp number of sequenced bases = 56,246,196 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,525 duplication rate = 7.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.2424 >>>>>>> ACTG content number of A's = 16,254,414 bp (28.9%) number of C's = 11,226,865 bp (19.96%) number of T's = 17,784,946 bp (31.62%) number of G's = 10,979,898 bp (19.52%) number of N's = 73 bp (0%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 33,649 >>>>>>> Coverage mean coverageData = 0.0182X std coverageData = 0.3886X There is a 1% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 0.01% 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% 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 3710628 0.014887136429642034 0.23893454509249273 chr2 243199373 4239178 0.017430875531081243 0.3518850146571317 chr3 198022430 3765416 0.01901509844112104 0.3016183596468396 chr4 191154276 5142808 0.02690396525579161 0.6658151010471663 chr5 180915260 4005288 0.0221390279625942 0.40347017859476625 chr6 171115067 5439944 0.03179114554535399 0.8060463893243215 chr7 159138663 2318176 0.014567019455228173 0.24455733194118498 chr8 146364022 2971564 0.020302557687298318 0.3805368436373272 chr9 141213431 2482180 0.0175775064908663 0.339276657655025 chr10 135534747 1871624 0.013809182083764837 0.18938342693004748 chr11 135006516 2450322 0.018149657309873845 0.3249481948716807 chr12 133851895 2725832 0.020364537984314677 0.33384033966556514 chr13 115169878 1606684 0.013950557453920372 0.21098645526442714 chr14 107349540 2051220 0.01910786017341108 0.47358359649015674 chr15 102531392 1589156 0.015499214133365125 0.3274193254017805 chr16 90354753 973332 0.010772338672654 0.25576228118895694 chr17 81195210 948816 0.011685615444556397 0.2611414210783406 chr18 78077248 1492044 0.019109843625635985 0.3937124276009959 chr19 59128983 558422 0.009444133344894499 0.18118153158263384 chr20 63025520 733362 0.011635953182139553 0.19101373278569395 chr21 48129895 465962 0.00968134254188587 0.14360392261419846 chr22 51304566 626398 0.012209400621379391 0.4840415915614259 chrMT 16571 128 0.007724337698388752 0.08754811423160411 chrX 155270560 3930018 0.025310773658573784 0.335200779511324 chrY 59373566 147694 0.0024875379727065743 0.057319979739004004