BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237603.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 = 918,258 number of mapped reads = 697,704 (75.98%) number of supplementary alignments = 4,484 (0.49%) number of secondary alignments = 0 number of mapped bases = 45,146,011 bp number of sequenced bases = 45,123,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,628 duplication rate = 1.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9489 >>>>>>> ACTG content number of A's = 13,322,299 bp (29.52%) number of C's = 7,996,739 bp (17.72%) number of T's = 13,467,190 bp (29.84%) number of G's = 10,261,362 bp (22.74%) number of N's = 76,338 bp (0.17%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 444,963 number of insertions = 3,490 mapped reads with insertion percentage = 0.5% number of deletions = 14,053 mapped reads with deletion percentage = 1.99% homopolymer indels = 47.61% >>>>>>> Coverage mean coverageData = 0.0146X std coverageData = 0.1404X There is a 1.35% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3714991 0.014904640899570717 0.16571052780763407 chr2 243199373 4053325 0.016666675370088226 0.15397599565211217 chr3 198022430 3165648 0.015986310237683682 0.13685383153899683 chr4 191154276 3047759 0.01594397501209965 0.13558349222064947 chr5 180915260 2737462 0.015131183516525913 0.13045925653351148 chr6 171115067 2528422 0.014776150600461151 0.13536962114280604 chr7 159138663 2663143 0.01673473277829411 0.16675155170909686 chr8 146364022 2461818 0.016819830217565352 0.15407686157875503 chr9 141213431 1846058 0.013072821663826013 0.13416373706104495 chr10 135534747 2021870 0.014917724382515724 0.14028869433538613 chr11 135006516 1992270 0.014756843291919333 0.14073360374015617 chr12 133851895 2406036 0.01797536000517587 0.14693528920891044 chr13 115169878 1618877 0.014056427150161607 0.12847533915349166 chr14 107349540 1295658 0.012069525402717142 0.11857971017919207 chr15 102531392 1326101 0.012933609640255347 0.12322395835436731 chr16 90354753 1058461 0.011714502722396906 0.11853887885531285 chr17 81195210 934092 0.011504274697977874 0.11676340974410573 chr18 78077248 1224330 0.015681008633910868 0.18437628997512323 chr19 59128983 631477 0.01067965265020709 0.12551129328833432 chr20 63025520 864539 0.01371728468087213 0.12640007174665638 chr21 48129895 580528 0.012061692634068701 0.12227921789046528 chr22 51304566 394223 0.0076839749506895745 0.09398175147856903 chrMT 16571 30928 1.866393096373182 1.6041877873633894 chrX 155270560 2432276 0.01566475962990022 0.13610407029209687 chrY 59373566 115719 0.0019489986503421406 0.051890379740250375