BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525139.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 965,829 number of mapped reads = 834,155 (86.37%) number of supplementary alignments = 19,920 (2.06%) number of secondary alignments = 0 number of mapped bases = 62,970,569 bp number of sequenced bases = 62,944,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,544 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5884 >>>>>>> ACTG content number of A's = 16,335,916 bp (25.95%) number of C's = 12,217,030 bp (19.41%) number of T's = 20,115,960 bp (31.96%) number of G's = 14,273,468 bp (22.68%) number of N's = 2,431 bp (0%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 503,407 number of insertions = 5,491 mapped reads with insertion percentage = 0.65% number of deletions = 15,064 mapped reads with deletion percentage = 1.78% homopolymer indels = 43.41% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.2402X There is a 1.87% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 6060709 0.02431572276804879 0.40351357452501907 chr2 243199373 5262024 0.021636667624138982 0.33116014203814814 chr3 198022430 4041303 0.02040830930112311 0.1511328908570282 chr4 191154276 4098233 0.02143940007912771 0.16148881033705656 chr5 180915260 3719492 0.020559304947520736 0.15246830818947493 chr6 171115067 3495198 0.02042600959271459 0.1672341351498037 chr7 159138663 3370222 0.021177895656946673 0.33337440457554135 chr8 146364022 3157538 0.0215731841531384 0.2989490199363119 chr9 141213431 2556698 0.018105204171407745 0.2225096043127636 chr10 135534747 2835213 0.020918716880771543 0.24866141702677227 chr11 135006516 3404535 0.02521756061018566 0.25209423915707535 chr12 133851895 2728106 0.020381526910769547 0.15206094446704127 chr13 115169878 2234810 0.019404466157374935 0.14756537301672965 chr14 107349540 1872636 0.017444285275931316 0.15256052833510414 chr15 102531392 1719491 0.016770385795601018 0.13626210380396925 chr16 90354753 1371929 0.015183805549222187 0.1424733169685011 chr17 81195210 1861194 0.022922460573721035 0.17954481951309575 chr18 78077248 1668197 0.021365981034577448 0.342362680871346 chr19 59128983 1173992 0.01985476394884045 0.29352440313065203 chr20 63025520 1219504 0.01934936831937285 0.1485768077696995 chr21 48129895 783322 0.01627516536240106 0.1413623332401282 chr22 51304566 633284 0.012343618694679145 0.11615448872244317 chrMT 16571 1372 0.08279524470460443 0.29767924632954873 chrX 155270560 3548176 0.0228515695441557 0.19647403462596522 chrY 59373566 153391 0.002583489763778042 0.07191969182934276