BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006443.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,496,869 number of mapped reads = 1,416,105 (94.6%) number of supplementary alignments = 4,664 (0.31%) number of secondary alignments = 0 number of mapped bases = 78,988,993 bp number of sequenced bases = 78,964,076 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,610 duplication rate = 1.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4951 >>>>>>> ACTG content number of A's = 22,583,757 bp (28.6%) number of C's = 16,318,274 bp (20.67%) number of T's = 23,016,341 bp (29.15%) number of G's = 17,043,980 bp (21.58%) number of N's = 1,724 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 321,652 number of insertions = 4,877 mapped reads with insertion percentage = 0.34% number of deletions = 15,047 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2489X There is a 2.36% of reference with a coverageData >= 1X There is a 0.15% 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 6169105 0.024750610350535496 0.3105423219587729 chr2 243199373 6719701 0.02763042074125742 0.20720804668468099 chr3 198022430 5607210 0.02831603470374543 0.17712849688732601 chr4 191154276 5138352 0.026880654241812515 0.18043647492712367 chr5 180915260 4866991 0.026902047953279343 0.1729367087903008 chr6 171115067 4414948 0.025801047665779193 0.17456080476705035 chr7 159138663 4331659 0.027219400479693612 0.2274083458638666 chr8 146364022 4122499 0.02816606802455866 0.6970198440166472 chr9 141213431 3382045 0.02394988193438909 0.18434966183869397 chr10 135534747 3465748 0.025570918725365682 0.22474822484596751 chr11 135006516 3707201 0.027459422773342287 0.19633235885352981 chr12 133851895 3706365 0.02769004503074088 0.1768598640291226 chr13 115169878 2684112 0.023305677201464085 0.16062528809690302 chr14 107349540 2486586 0.02316345277306265 0.16365840933983905 chr15 102531392 2416524 0.023568625694655544 0.16173557018886828 chr16 90354753 2192952 0.024270466435783407 0.18128826200329512 chr17 81195210 2232187 0.02749160941883148 0.1871423146981636 chr18 78077248 2218319 0.028411849249604697 0.2658024015138942 chr19 59128983 1632411 0.027607628563474533 0.26130329850020145 chr20 63025520 1783002 0.028290159287856727 0.17980407542713664 chr21 48129895 1530661 0.031802708067408 0.20047726622368364 chr22 51304566 1002615 0.01954241265777397 0.1580801640328779 chrMT 16571 28500 1.7198720656568705 1.5216706460638503 chrX 155270560 2495650 0.016072911696847103 0.13942798610585025 chrY 59373566 653650 0.01100910799260398 0.16472392618753404