BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212162.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,937,852 number of mapped reads = 4,249,965 (86.07%) number of supplementary alignments = 35,485 (0.72%) number of secondary alignments = 0 number of mapped bases = 287,027,870 bp number of sequenced bases = 286,894,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,899 duplication rate = 4.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2038 >>>>>>> ACTG content number of A's = 79,676,550 bp (27.77%) number of C's = 51,938,972 bp (18.1%) number of T's = 92,481,962 bp (32.24%) number of G's = 62,724,353 bp (21.86%) number of N's = 72,376 bp (0.03%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,460,666 number of insertions = 23,899 mapped reads with insertion percentage = 0.56% number of deletions = 78,599 mapped reads with deletion percentage = 1.83% homopolymer indels = 49.73% >>>>>>> Coverage mean coverageData = 0.0927X std coverageData = 0.7769X There is a 7.02% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 27327898 0.10964024037476722 1.5958581210129181 chr2 243199373 18003804 0.07402899019809561 0.7273107694501236 chr3 198022430 17656895 0.089166136381621 0.3848253354615687 chr4 191154276 12876953 0.06736419016857358 0.4068609603102623 chr5 180915260 21245903 0.11743566020909457 0.4333711756739356 chr6 171115067 19628179 0.11470748511000495 0.568413075055668 chr7 159138663 17491638 0.10991444612048802 1.1177107306532315 chr8 146364022 16844932 0.11508929428025694 1.0583313531515626 chr9 141213431 13362307 0.0946249015081292 0.6673159395747965 chr10 135534747 8471083 0.06250119019294735 0.8008533154142564 chr11 135006516 15598477 0.11553869740627927 0.7870156397214271 chr12 133851895 8216449 0.061384629631130734 0.3241843508134812 chr13 115169878 9627154 0.08359090212807206 0.35800455424199845 chr14 107349540 10167804 0.09471679152048532 0.41759835445043103 chr15 102531392 9124205 0.08898937995497028 0.3698685644555583 chr16 90354753 8187895 0.0906194165568689 0.4289394217067408 chr17 81195210 4733159 0.05829357421453803 0.42352717827046393 chr18 78077248 8721925 0.11170891935125582 1.203804462845088 chr19 59128983 6370255 0.10773489880588678 1.1560995842385144 chr20 63025520 6347342 0.10071066450542573 0.4097273939084319 chr21 48129895 4401246 0.09144516105842325 0.46390210773707913 chr22 51304566 1728491 0.03369078299970416 0.22109410681020153 chrMT 16571 69349 4.1849616800434495 2.7812080209333185 chrX 155270560 20041499 0.12907468743591832 0.5198326043162455 chrY 59373566 783028 0.013188158514851542 0.32113478473751955