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
A1 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,963,768	C→G	100%	V365L (GTA→CTA)	hemY ←	Protoporphyrinogen oxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,963,768	0	C	G	100.0%	143.1 / NA	43	V365L (GTA→CTA)	hemY	Protoporphyrinogen oxidase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (26/17); total (26/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGT  >  USA300TCH1516_ALE/1963636‑1963902

tCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCAc                                                                                                                                >  2:366436/1‑141 (MQ=255)

      aaCGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCa                                                                                                                          >  1:344372/1‑141 (MQ=255)

       aCGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGACCGAATCaa                                                                                                                         >  1:322675/1‑141 (MQ=255)

              aCAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacctta                                                                                                                  <  1:123342/141‑1 (MQ=255)

                aaTTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacc                                                                                                                <  1:245681/141‑1 (MQ=255)

                 aTTGTAAATTCAGTATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct                                                                                                               <  1:276529/141‑1 (MQ=255)

                  ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACTTGGTATACCTAGATACGCACGAATAAAAaacttacatt                                                                                                              >  1:151337/1‑141 (MQ=255)

                  ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacctt                                                                                                              <  1:355875/141‑1 (MQ=255)

                         ttCAGGATCACCTTTCAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCAGTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGgtgt                                                                                                       >  1:294896/1‑141 (MQ=255)

                         gtCAGGATCACCTTTAACTGTCATCATTTGACTTAAACCTCTACGTACAATCGATACTAATTCATTATCGGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGgtgt                                                                                                       <  2:113023/140‑1 (MQ=255)

                             ggATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACNTGGTTTACCTAGATACGCACGNANCAAAANCNTACCTTCCGGTggagta                                                                                                   >  1:320741/1‑141 (MQ=255)

                                  aCCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTGGTAAATgg                                                                                              >  1:131013/1‑141 (MQ=255)

                                   ccTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAACCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGc                                                                                             <  2:303749/141‑1 (MQ=255)

                                       tAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGATTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtt                                                                                         >  1:335131/1‑141 (MQ=255)

                                                      gACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                                                                          <  1:113237/141‑1 (MQ=255)

                                                                  tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTaa                                                              >  1:126923/1‑141 (MQ=255)

                                                                   aCGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAAt                                                             <  1:236402/141‑1 (MQ=255)

                                                                       aCAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACTTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTGATGTCt                                                         >  2:19562/1‑141 (MQ=255)

                                                                        cAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCCAGTACATGCGGTAATGTCTg                                                        <  1:241435/141‑1 (MQ=255)

                                                                               tACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTGGAATGTCCAAGTACATGCGGTAATGTCTGTATCAcc                                                 >  1:268045/1‑140 (MQ=255)

                                                                                   aaTTCATTATCTGTATGATCATCAACCACAGTCTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGtt                                             <  1:264661/141‑1 (MQ=255)

                                                                                    aTTCATTATCTGTATGATCATCAACCACAGTATCACGTGGTTTACCTAGATACGTACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGCTGTCCAAGTACATGCGGTTATCTCTGTATCACTCGTtc                                            <  1:221299/141‑1 (MQ=255)

                                                                                          tATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATTTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCaa                                      >  1:371550/1‑141 (MQ=255)

                                                                                           aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAt                                     >  2:77510/1‑141 (MQ=255)

                                                                                           aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAt                                     <  1:173350/141‑1 (MQ=255)

                                                                                             cTGTATGATCAGCAACCACTGTATGACCTGGTTTACCTAGACACGGACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCCGTAAGGTCTGTATCACTCGTTCTCGCAATTa                                   <  2:26700/141‑1 (MQ=255)

                                                                                              tGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTAc                                  >  1:129742/1‑141 (MQ=255)

                                                                                                tATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGa                                >  2:371996/1‑141 (MQ=255)

                                                                                                    atcatcAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGcc                            >  1:50964/1‑141 (MQ=255)

                                                                                                      catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGCTGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTTCGAAGCCAg                          >  1:338010/1‑141 (MQ=255)

                                                                                                      catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAg                          >  2:85467/1‑141 (MQ=255)

                                                                                                      catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAg                          >  1:64594/1‑141 (MQ=255)

                                                                                                       atcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGACGTAAATGGCCATTTTTTCGATGTCAAAGTACATGCGGTAATGCTCGTATCCCTCGTTTTCGCAATTGCGAAGCCCGt                         >  2:105917/1‑141 (MQ=255)

                                                                                                         caACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAACTGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATCTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTAc                       <  2:294896/141‑1 (MQ=255)

                                                                                                           aCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACca                     >  2:245913/1‑141 (MQ=255)

                                                                                                           aCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACca                     >  2:185011/1‑141 (MQ=255)

                                                                                                            ccACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTACCGAGTATTTAATGGCCATTTTTTCTTTGTCTAAGTAGATGCGGTAATGTCTGTATCCCTCGTTCTCGCAATTACGAAGCCAGTAGcat                    >  2:83346/1‑141 (MQ=255)

                                                                                                               caGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCTCAATTACGAAGCCCGTACcatcat                 >  1:244767/1‑141 (MQ=255)

                                                                                                               caGTATCACCTGGGTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcatcat                 <  2:284769/141‑1 (MQ=255)

                                                                                                                 gTATCACCTGGTTTACATAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATgg               >  1:220917/1‑141 (MQ=255)

                                                                                                                      cccTCGTTTACCTAGATACGCACGAATCAAACCCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTCTTGTCTATATCACGCGTTCTCCGAATTACGAAGCCAGTACCATCATGGGTAtt          <  2:180875/140‑1 (MQ=255)

                                                                                                                      aCCTGTTTTACCTGGATACGCACGCATCAAAACCTTGCCTTCCGGTGTAGTACATGGCCATTTTTTCGATGTCCAAGGACATGCGGTCATGCCTGTATCACTCGTTCTCGCAATTACGTAGCCAGTACCATCATGGGTAtt          <  2:230934/141‑1 (MQ=255)

                                                                                                                              tACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGt  >  2:149047/1‑141 (MQ=255)

TCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGT  >  USA300TCH1516_ALE/1963636‑1963902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A