BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231744.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 869,466 number of mapped reads = 671,563 (77.24%) number of supplementary alignments = 5,928 (0.68%) number of secondary alignments = 0 number of mapped bases = 44,072,626 bp number of sequenced bases = 44,045,282 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,810 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1072 >>>>>>> ACTG content number of A's = 12,632,698 bp (28.68%) number of C's = 7,440,355 bp (16.89%) number of T's = 14,749,248 bp (33.49%) number of G's = 9,221,027 bp (20.94%) number of N's = 1,954 bp (0%) GC percentage = 37.83% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 398,896 number of insertions = 3,974 mapped reads with insertion percentage = 0.59% number of deletions = 15,526 mapped reads with deletion percentage = 2.27% homopolymer indels = 44.41% >>>>>>> Coverage mean coverageData = 0.0142X std coverageData = 0.3595X There is a 1.2% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.03% 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 1926307 0.007728393984623212 0.16645671606207915 chr2 243199373 1526313 0.006275974239456613 0.1359256897279457 chr3 198022430 4523836 0.02284506861167192 0.17273431082797303 chr4 191154276 1929880 0.010095929007625234 0.12616458422721308 chr5 180915260 3462610 0.01913940261313501 0.15991180554940743 chr6 171115067 3559393 0.020801166503940885 0.16888442578290758 chr7 159138663 2640639 0.01659332151106485 0.18804557715583814 chr8 146364022 2995319 0.020464858501906977 1.5036884973322548 chr9 141213431 1938257 0.01372572698130959 0.14721452722614153 chr10 135534747 2070937 0.015279749627599187 0.17430153258964404 chr11 135006516 1951704 0.014456368905927474 0.1429895209231876 chr12 133851895 1440229 0.01075987007879119 0.12031208591717452 chr13 115169878 2245880 0.019500585040126552 0.16211272781300992 chr14 107349540 2891052 0.026931200636723735 0.1912254649020473 chr15 102531392 233443 0.002276795383798164 0.053425080583075414 chr16 90354753 758327 0.008392773759228804 0.1089644481197009 chr17 81195210 562206 0.0069241276671370144 0.09570177203373577 chr18 78077248 1103413 0.014132324438484308 0.21228419103586416 chr19 59128983 1148332 0.019420797411651744 0.1796019227799802 chr20 63025520 1416256 0.022471151368525004 0.1747890461605157 chr21 48129895 971964 0.020194600466092852 0.16840909185073913 chr22 51304566 236551 0.004610720223225356 0.0745955701603887 chrMT 16571 41256 2.4896505944119243 2.1669028905345176 chrX 155270560 2359350 0.015195089139885888 0.14363388720430134 chrY 59373566 139172 0.0023440060851322286 0.07085877676476184