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
A3 F67 I1 R2	13	27.5	561530	92.1%	517169	135.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,030,815	G→T	A90S (GCA→TCA)	USA300HOU_1885 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,030,815	0	G	T	100.0%	116.3 / NA	35	A90S (GCA→TCA)	USA300HOU_1885	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (19/16); total (19/16)

ACAATTGAACCAACTGCCAAGGCATCACTTATTAAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTGCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGAACATTGACAGC  >  CP000730/2030680‑2030951

acaATTGAACCAACTGCCAAGGCATCACTTATTAAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACg                                                                                                                                     <  2:96090/141‑1 (MQ=255)

 caATTGAACCAACTGCCAAGGCATCACTTATTAAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGt                                                                                                                                    >  2:234228/1‑141 (MQ=255)

            aCTGCCACGGCATCACTTATTCAAGGTTATCGTAGATTACCTTCTACGGTAATTTGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTCTTACATATGCATTGAGTTCAACGTTCACGATTTTa                                                                                                                         >  2:234594/1‑141 (MQ=255)

            aCTGCCAAGGCATCACTTATTAAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTa                                                                                                                         >  2:234625/1‑141 (MQ=255)

                     gCATCACTTATTAAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACa                                                                                                                >  2:157691/1‑141 (MQ=255)

                               ttaAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAAt                                                                                                      <  1:270290/141‑1 (MQ=255)

                                         tCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGTTTTTATTCTTTACAAAACTCAAATTGCAAGTTgg                                                                                            <  1:7656/141‑1 (MQ=255)

                                         tCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTgg                                                                                            <  2:204435/141‑1 (MQ=255)

                                          cGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGt                                                                                           >  2:225788/1‑141 (MQ=255)

                                           gTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTa                                                                                          <  2:156622/141‑1 (MQ=255)

                                               aTTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGaa                                                                                      >  2:81677/1‑141 (MQ=255)

                                                  aCCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATTTTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTAGTAcagcgac                                                                                   <  1:213017/141‑7 (MQ=255)

                                                          cGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTAc                                                                           <  2:15833/141‑1 (MQ=255)

                                                           ggTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACt                                                                          >  1:162873/1‑141 (MQ=255)

                                                             tAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTaa                                                                        >  1:10416/1‑141 (MQ=255)

                                                               aTTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAAca                                                                      >  2:183434/1‑141 (MQ=255)

                                                                     gCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACACAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTa                                                                >  2:242093/1‑141 (MQ=255)

                                                                     gCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTa                                                                >  2:241855/1‑141 (MQ=255)

                                                                             tGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGAt                                                        >  1:227915/1‑141 (MQ=255)

                                                                                             tatttattCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCatgat                                        >  1:94455/1‑141 (MQ=255)

                                                                                                ttattCGGCGATCAATCACCTTTTACATATTCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGcc                                     <  1:75746/141‑1 (MQ=255)

                                                                                                    tCGGCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACa                                 <  2:162873/141‑1 (MQ=255)

                                                                                                       gCGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACatat                              <  2:3853/141‑1 (MQ=255)

                                                                                                        cGATCAATCACCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATAtt                             <  1:81677/141‑1 (MQ=255)

                                                                                                           tcaatcaCCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCAGTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCaa                          >  2:246656/1‑141 (MQ=255)

                                                                                                              atcaCCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACtt                       >  1:226026/1‑141 (MQ=255)

                                                                                                                caCCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGt                                                                                   <  1:236187/79‑1 (MQ=255)

                                                                                                                caCCTTTTACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGt                                                                                   >  2:236187/1‑79 (MQ=255)

                                                                                                                    ttttACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGtc                 <  2:41562/141‑1 (MQ=255)

                                                                                                                    ttttACATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGtc                 <  1:229957/141‑1 (MQ=255)

                                                                                                                        aCATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGa             >  2:33537/1‑141 (MQ=255)

                                                                                                                         cATATGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGaa            >  2:135920/1‑141 (MQ=255)

                                                                                                                            atGCATTGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGAACAt         <  1:135192/141‑1 (MQ=255)

                                                                                                                                 ttGAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGAACATTGACa    <  1:22151/141‑1 (MQ=255)

                                                                                                                                   gAGTTCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGAACATTGACAGc  >  1:11893/1‑141 (MQ=255)

ACAATTGAACCAACTGCCAAGGCATCACTTATTAAAGGTTATCGTAGATTACCTGCTACGGTAATTGGTGCAGGCTTTGCAGTATTATTTACATATTTATTCGGCGATCAATCACCTTTTACATATGCATTGAGTGCAACGTTCACGATTTTATTCTGTACAAAACTCAAATTGCAAGTTGGTACGAATGTCGCTGTACTAACATCATTAGCTATGATTCCAGGTATTCATGATGCCTACATATTCAACTTTTTGTCTCGAACATTGACAGC  >  CP000730/2030680‑2030951

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A