BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124929.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 1,743,620 number of mapped reads = 1,718,073 (98.53%) number of supplementary alignments = 13,144 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 860,005 number of mapped paired reads (second in pair) = 858,068 number of mapped paired reads (both in pair) = 1,713,126 number of mapped paired reads (singletons) = 4,947 number of mapped bases = 233,160,461 bp number of sequenced bases = 233,016,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 234,232 duplication rate = 13.73% >>>>>>> Insert size mean insert size = 54,572.0405 std insert size = 2,179,074.4473 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 53.731 >>>>>>> ACTG content number of A's = 68,246,232 bp (29.29%) number of C's = 46,825,986 bp (20.1%) number of T's = 68,240,633 bp (29.29%) number of G's = 49,679,895 bp (21.32%) number of N's = 24,001 bp (0.01%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 2,605,491 number of insertions = 41,075 mapped reads with insertion percentage = 2.32% number of deletions = 80,862 mapped reads with deletion percentage = 4.56% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.0753X std coverageData = 0.8117X There is a 4.44% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.15% 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 0.01% 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 18814455 0.07548408475178885 1.0615882694462282 chr2 243199373 19817868 0.08148815416559482 0.8467054459447193 chr3 198022430 13559733 0.06847574287417844 0.36471903463420985 chr4 191154276 10085322 0.05276011717362786 0.45348455082402234 chr5 180915260 11885439 0.06569616626038069 0.34957336080641976 chr6 171115067 15674720 0.09160338873022794 0.6199804540387663 chr7 159138663 17887861 0.11240424333588878 1.2005378599449448 chr8 146364022 14993151 0.10243740773945116 0.5117359388841377 chr9 141213431 9671281 0.06848697699300288 1.0635860183290766 chr10 135534747 10612389 0.07830013509377046 1.8973622131790084 chr11 135006516 14751244 0.10926320030360609 0.7379939596379328 chr12 133851895 7241650 0.054101960977093376 0.31581916544316585 chr13 115169878 10607605 0.09210398746797319 0.5076023644607758 chr14 107349540 3566705 0.03322515401556448 0.25683003597217086 chr15 102531392 4673309 0.04557929926475591 0.2896079022678364 chr16 90354753 6579367 0.0728170547929006 1.0532079400113301 chr17 81195210 4944231 0.060893136430092365 0.9293580724935994 chr18 78077248 6250667 0.0800574707756093 1.1667196845685377 chr19 59128983 3603368 0.06094080799597044 0.6414712602789816 chr20 63025520 5765969 0.09148625826490603 0.4333981748651772 chr21 48129895 1862503 0.038697424958022454 0.31342398007488526 chr22 51304566 1632823 0.03182607567521378 0.2402847353326512 chrMT 16571 96586 5.828616257317 4.343314622848812 chrX 155270560 18156694 0.11693584411623169 0.5634345759623569 chrY 59373566 425521 0.007166842564248204 0.4235159477131802