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
A5 F18 I0 R1	32	69.1	1533550	96.6%	1481409	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,416,458	A→T	100%	I216N (ATT→AAT)	oppD_4 ←	Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,416,458	0	A	T	100.0%	143.3 / NA	44	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (23/21); total (23/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416328‑1416593

tCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACTTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                               <  1:143659/141‑1 (MQ=255)

    tCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAatat                                                                                                                           <  1:270999/141‑1 (MQ=255)

    tCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCATTTAAAACATAATTGTACTGACAatat                                                                                                                           <  2:737266/141‑1 (MQ=255)

       tAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                        <  2:232823/141‑1 (MQ=255)

       tAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATGAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAAAATAATTGTACTGACAATATTTc                                                                                                                        >  1:114824/1‑141 (MQ=255)

         gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCaa                                                                                                                      >  1:742399/1‑141 (MQ=255)

            aTCCCTCTTTAATTGCGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATAc                                                                                                                   <  2:690233/141‑1 (MQ=255)

               ccTCTTTAATTTGGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATg                                                                                                                <  2:697079/141‑1 (MQ=255)

                     tAATTTTGTTCTATATTTAATTAGACGTTAAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                          <  2:54015/141‑1 (MQ=255)

                     tAATTGTGTTCTATATTTCATTGGACGTACAGTATACATATGCAAATGCGCATACTTGAAATGAATAATATTACCTCGTTCAATGATTTGACCTTCTTCTAAAACATAATTGTACTGACAATAGTTCAATACATGACTTaa                                                                                                          <  2:666198/141‑1 (MQ=255)

                        ttGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATTACTTCAGtt                                                                                                       >  2:172991/1‑141 (MQ=255)

                         tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGCCAATATTTCCATACATGACTTAAGTTa                                                                                                      >  2:223300/1‑141 (MQ=255)

                          gtgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                     >  1:598216/1‑141 (MQ=255)

                             ttCTATATTTAATTAGACGTTCAGGATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtg                                                                                                  <  1:48123/141‑1 (MQ=255)

                                  tatTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATCCATGACTTAAGTTATATGTGata                                                                                             >  2:25182/1‑141 (MQ=255)

                                  aatTTAATTAGACGTTCAGTATACGGATGCAAATTCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAACTTAAGTCAtgtattgaa                                                                                             <  2:61090/140‑7 (MQ=255)

                                   atTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataa                                                                                            >  1:1613/1‑141 (MQ=255)

                                         ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATattaaata                                                                                      >  2:203058/1‑141 (MQ=255)

                                          tAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAATTAAGTTATGTGTGATaataaatca                                                                                     >  1:633281/1‑139 (MQ=255)

                                           aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataat                                                                                    >  1:640408/1‑141 (MQ=255)

                                              cGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGtt                                                                                 <  2:119424/141‑1 (MQ=255)

                                                  cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTAATGTGTGATAATAAATAATGTTTGAc                                                                             >  2:761664/1‑141 (MQ=255)

                                                   aggataCGGATGCAAATTCCCATCGTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTGTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAcc                                                                            <  1:601642/138‑1 (MQ=255)

                                                    gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                           <  1:604164/141‑1 (MQ=255)

                                                    gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAAAATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                           >  2:523542/1‑141 (MQ=255)

                                                               cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACTATGTTCTAATAc                                                                <  1:400129/141‑1 (MQ=255)

                                                                 aaggCTCATACTTGAAATGCTTCATATTACTTCGTTCAGTGATTTGACCTTCTTTTAAAACATAATTGTACTGAGAATATTTCATTACATCCCTTAAGCTAGGTGTGTTTATAAATAATGTTTGGGCGTGTTCTAGTACaa                                                              <  2:383610/138‑1 (MQ=255)

                                                                 aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCCATACATGACTTAAGTTATGTGTGATAATAAATCATGTTTGACCATCTTCTAcaacaa                                                              >  2:626040/1‑141 (MQ=255)

                                                                  aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAat                                                             >  1:454037/1‑141 (MQ=255)

                                                                         tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGATGt                                                      >  2:198600/1‑141 (MQ=255)

                                                                           cTTGCAAGGATTAATATTACCTCGTTCAACGACTTGACCTTGTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaa                                                    <  1:51127/141‑1 (MQ=255)

                                                                                 aTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTGCTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATc                                              >  1:147948/1‑141 (MQ=255)

                                                                                     ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATc                                          >  1:641136/1‑141 (MQ=255)

                                                                                     ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCGTTAATAAATCCATc                                          >  2:56030/1‑141 (MQ=255)

                                                                                           tttcctcctCCAATCATTTTACCTTCTTTTAAAACATAATTGAACTGAAAATATTCCCAAACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAACACAATAGGCTGTAATAAATCCATCACTTGa                                    <  1:126396/138‑1 (MQ=255)

                                                                                              ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                 <  2:454037/141‑1 (MQ=255)

                                                                                              ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                 <  2:598216/141‑1 (MQ=255)

                                                                                                     cAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                          >  2:567792/1‑141 (MQ=255)

                                                                                                      aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                         >  1:505953/1‑141 (MQ=255)

                                                                                                      aaTGATTTGACCTTCATTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                         >  1:569066/1‑141 (MQ=255)

                                                                                                          aTTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCa                     <  1:354778/141‑1 (MQ=255)

                                                                                                                         aaaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCAGCAGTTGATTACCGTTCAAAGCATCCAATGATGCAACt      >  1:713482/1‑141 (MQ=255)

                                                                                                                           aatctAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTgg    <  1:172991/137‑1 (MQ=255)

                                                                                                                             cATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGtt  >  2:14083/1‑141 (MQ=255)

TCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416328‑1416593

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