BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975245.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,421,750 number of mapped reads = 2,397,672 (99.01%) number of supplementary alignments = 24,795 (1.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,198,352 number of mapped paired reads (second in pair) = 1,199,320 number of mapped paired reads (both in pair) = 2,387,740 number of mapped paired reads (singletons) = 9,932 number of mapped bases = 218,421,492 bp number of sequenced bases = 218,289,261 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,348 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 157,444.0476 std insert size = 3,876,619.2077 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.1239 >>>>>>> ACTG content number of A's = 63,898,144 bp (29.27%) number of C's = 42,893,481 bp (19.65%) number of T's = 63,947,102 bp (29.29%) number of G's = 47,547,506 bp (21.78%) number of N's = 3,028 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,840,163 number of insertions = 37,610 mapped reads with insertion percentage = 1.51% number of deletions = 68,619 mapped reads with deletion percentage = 2.79% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0706X std coverageData = 1.1113X There is a 4.98% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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% 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 17290260 0.06936897461130097 0.5742480248369399 chr2 243199373 20019208 0.08231603458944772 1.3562399699861303 chr3 198022430 14881000 0.07514805267261895 0.4351023047601177 chr4 191154276 14333999 0.07498654646888464 0.7033322087361185 chr5 180915260 13497919 0.07460906835609113 0.3762987071916795 chr6 171115067 12705241 0.07424969187546764 0.4062690652906972 chr7 159138663 11398080 0.07162357522131502 0.7893161337000593 chr8 146364022 11314957 0.07730695594030615 0.38981267753034604 chr9 141213431 9160862 0.06487245536863982 0.9318661820439649 chr10 135534747 13240399 0.09769007057651423 4.008849303364055 chr11 135006516 10337458 0.07657006718105369 0.5479237338465717 chr12 133851895 9538122 0.07125877448354392 0.34140000491448363 chr13 115169878 6565016 0.05700289098161587 0.3024210582625577 chr14 107349540 6324161 0.058911859333537896 0.37713306652236217 chr15 102531392 6310199 0.06154406837663923 0.31204648388760664 chr16 90354753 8383468 0.09278391807456991 1.8874259851363397 chr17 81195210 5285545 0.06509675878663286 0.8751164408351989 chr18 78077248 5978804 0.07657549610355119 0.9930712636913042 chr19 59128983 2813594 0.04758400799824343 0.3766399423190761 chr20 63025520 4627475 0.0734222422916939 0.3881887848624945 chr21 48129895 2767125 0.05749285345417853 0.3997430714786274 chr22 51304566 2286961 0.04457616891252915 0.3226575398582423 chrMT 16571 49685 2.9983103011284773 2.391636696924774 chrX 155270560 6819341 0.043919085498242555 0.31986541381430295 chrY 59373566 2492613 0.04198186445462952 1.1967752009194499