Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,619,957	G→A	128 (TAG→TAA)	marA →	multiple antibiotic resistance transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,619,957	0	G	A	100.0%	88.4 / NA	29	128 (TAG→TAA)	marA	multiple antibiotic resistance transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (15/14); total (15/14)

TGGCTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATG  >  NC_000913/1619825‑1620091

tGGCTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGaaa                                                                                                                                  <  2:349792/139‑1 (MQ=255)

              aacaaACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCa                                                                                                                    <  2:317049/139‑1 (MQ=255)

               acaaACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCAc                                                                                                                   <  2:203733/139‑1 (MQ=255)

                                                        cgccgcATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTg                                                                          <  2:334994/139‑1 (MQ=255)

                                                           cgcATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTgcgc                                                                       <  1:555860/139‑1 (MQ=255)

                                                             cATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCtt                                                                     >  2:397646/1‑139 (MQ=255)

                                                                     ccGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCtt                                                             >  2:410975/1‑139 (MQ=255)

                                                                        gATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTc                                                          >  2:661919/1‑139 (MQ=255)

                                                                        gATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTc                                                          >  2:482655/1‑139 (MQ=255)

                                                                         aTGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTcc                                                         <  1:627329/139‑1 (MQ=255)

                                                                                atatGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAgg                                                  >  2:683011/1‑139 (MQ=255)

                                                                                     cAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGtt                                             <  1:410975/139‑1 (MQ=255)

                                                                                      aGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTg                                            <  2:619758/139‑1 (MQ=255)

                                                                                       gggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTAtt                                                                  <  1:771563/116‑1 (MQ=255)

                                                                                       gggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGc                                           >  1:115226/1‑139 (MQ=255)

                                                                                       gggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGAAATCATGAAACCGCTTTCATCCGCAATAGCAGCTGCGCTTAtt                                                                  >  2:771563/1‑116 (MQ=255)

                                                                                        ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCg                                          >  1:714407/1‑139 (MQ=255)

                                                                                        ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCg                                          >  1:347495/1‑139 (MQ=255)

                                                                                            aaTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAAc                                      >  2:197118/1‑139 (MQ=255)

                                                                                             aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACa                                     >  1:363988/1‑139 (MQ=255)

                                                                                                       ttACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAGCCCCGCAg                           <  1:348938/139‑1 (MQ=255)

                                                                                                          cATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCa                        <  1:197118/139‑1 (MQ=255)

                                                                                                           aTCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAg                       <  1:422132/139‑1 (MQ=255)

                                                                                                                 tAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTa                 <  2:149265/139‑1 (MQ=255)

                                                                                                                        ttACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTtg          >  2:85872/1‑139 (MQ=255)

                                                                                                                         tACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCgcgc                                                     >  1:763017/1‑95 (MQ=255)

                                                                                                                         tACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCgcgc                                                     <  2:763017/95‑1 (MQ=255)

                                                                                                                         tACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTtgt         >  1:138764/1‑139 (MQ=255)

                                                                                                                                gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATg  >  1:663628/1‑139 (MQ=255)

TGGCTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATG  >  NC_000913/1619825‑1620091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A