BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819017.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,770,889 number of mapped reads = 2,722,565 (98.26%) number of supplementary alignments = 37,253 (1.34%) number of secondary alignments = 0 number of mapped bases = 252,081,133 bp number of sequenced bases = 251,928,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,445,097 duplication rate = 42.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1632 >>>>>>> ACTG content number of A's = 74,417,562 bp (29.54%) number of C's = 53,381,829 bp (21.19%) number of T's = 69,287,970 bp (27.5%) number of G's = 54,828,422 bp (21.76%) number of N's = 12,378 bp (0%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,591,917 number of insertions = 41,254 mapped reads with insertion percentage = 1.47% number of deletions = 79,808 mapped reads with deletion percentage = 2.87% homopolymer indels = 40.03% >>>>>>> Coverage mean coverageData = 0.0814X std coverageData = 1.0568X There is a 3.08% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 25735044 0.10324966853342363 1.7470264500696906 chr2 243199373 20775514 0.08542585346221267 1.7247069698027189 chr3 198022430 13542228 0.06838734379736679 0.5655968988261663 chr4 191154276 13952524 0.07299090709328417 0.6652137899763783 chr5 180915260 13743198 0.0759648356915829 0.6247121657187523 chr6 171115067 10590596 0.06189166264359409 0.6496453069841103 chr7 159138663 12427158 0.07809012445957272 1.1929982485097668 chr8 146364022 20549453 0.140399619518518 0.9034120490043979 chr9 141213431 11043568 0.07820479908883454 0.9532006275966156 chr10 135534747 13449485 0.09923274509082161 1.3269370333635948 chr11 135006516 8215194 0.060850351845239826 0.623157010703154 chr12 133851895 11644871 0.086998178098263 0.6581984598185393 chr13 115169878 5401331 0.04689881672011496 0.46540846806721564 chr14 107349540 5964726 0.05556359160924211 0.5540741603765387 chr15 102531392 6759620 0.06592732106865379 0.567976001338378 chr16 90354753 8458621 0.09361567287998673 1.3752144694755661 chr17 81195210 9071156 0.11172033424139183 0.8346656087390655 chr18 78077248 5886600 0.07539456308705962 1.0682573109550622 chr19 59128983 5377421 0.09094391155011071 1.6702402485724168 chr20 63025520 7564706 0.12002607832509751 0.839051057185237 chr21 48129895 3591681 0.07462474206519669 0.6707768579002554 chr22 51304566 2179798 0.042487407456092696 0.51753643595464 chrMT 16571 38775 2.3399312051173737 3.263676149404327 chrX 155270560 15103372 0.09727131788537376 0.8117764590746145 chrY 59373566 1014493 0.017086610563360805 1.3148382633793283