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 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	100%	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	100.0%	143.1 / NA	51	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (29/22); total (29/22)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTG  >  USA300TCH1516_ALE/2279569‑2279840

tgtgCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtg                                                                                                                                      >  2:458515/1‑140 (MQ=255)

       ttattaGTTGATTCAACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTc                                                                                                                               >  2:373072/1‑140 (MQ=255)

         attaGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAc                                                                                                                             >  1:446425/1‑140 (MQ=255)

          ttaGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGCTGTTACTGTTCTTTCAcc                                                                                                                            >  2:2530/1‑140 (MQ=255)

             gTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATAAGTTGCTGATGTTACTTTTGTTTCACCTGt                                                                                                                         >  2:226943/1‑140 (MQ=255)

              ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTTTCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGtt                                                                                                                        <  1:1024/140‑1 (MQ=255)

                aaatCTACTCCTGCTTTACCAGTTACAACGTCATCCATTGCCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGc                                                                                                                      <  2:94212/137‑1 (MQ=255)

                  ttcttcttcTGGTTTACTAGTTACATTGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCg                                                                                                                    <  2:101435/140‑1 (MQ=255)

                       cTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCa                                                                                                               >  1:197696/1‑140 (MQ=255)

                                 aCTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGTGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTg                                                                                                     <  1:190047/140‑1 (MQ=255)

                                 aCTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTg                                                                                                     <  1:7503/140‑1 (MQ=255)

                                   tAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGgt                                                                                                   >  1:440848/1‑140 (MQ=255)

                                    aGTTACATCGTTTTCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGgtg                                                                                                  <  2:210424/140‑1 (MQ=255)

                                      ttACATGGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgtt                                                                                                >  2:392275/1‑140 (MQ=255)

                                        aCATCGGTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCCCATCCCTATCATTTGGtgttgt                                                                                              <  2:416183/140‑1 (MQ=255)

                                           tCGTTATCCATTGTCCGACTGTTTGATGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCgg                                                                                           >  1:275946/1‑140 (MQ=255)

                                            cGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTCGCTTGCGGTCTATAATTTGCATCATCAGTTTTTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGga                                                                                          >  2:265323/1‑140 (MQ=255)

                                                 tCCATTGTCGTATTGTTTGTTGATGCATCTACACTAGAATTTTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGc                                                                                     <  1:220540/140‑1 (MQ=255)

                                                 tCCATTGTCGGACTGTTTGTTGATGCATCTACACTATAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGc                                                                                     <  1:482572/140‑1 (MQ=255)

                                                 tCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCCCTCTTATTTGGTGTTGTCGGGGAAGc                                                                                     >  2:533711/1‑140 (MQ=255)

                                                   cATTGTCGGACTGTTTGTTGTTGCATCTTCTCTAGTATTGTTATTTGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGt                                                                                   <  1:232796/140‑1 (MQ=255)

                                                   cATTGTCGGACTGTTTGTAAATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGt                                                                                   >  2:529990/1‑140 (MQ=255)

                                                     ttGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATAACTATTATTTGGTGTTGTCGGAGAAGCGtgt                                                                                 >  1:184584/1‑138 (MQ=255)

                                                      tGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCAGTGGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTg                                                                                <  1:242130/140‑1 (MQ=255)

                                                       gTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCTGAGAAGCGTCTGc                                                                               >  1:271094/1‑140 (MQ=255)

                                                          ggACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGGTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTAGTTGGTGTTGTCGGGGAAGCGTCTGCgtt                                                                            >  2:293600/1‑140 (MQ=255)

                                                            aCTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGc                                                                          <  2:355025/140‑1 (MQ=255)

                                                            aCTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTACATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGc                                                                          >  1:144423/1‑140 (MQ=255)

                                                                        tGCATCTACACTAGAATTGTTATTTGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtcg                                                              <  2:383154/140‑1 (MQ=255)

                                                                         gCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCACTTGCTGATGTTACTGTTGTTTCACCTGTTCCTGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtcgt                                                             >  2:232436/1‑140 (MQ=255)

                                                                            tCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGactc                                                          >  2:178796/1‑140 (MQ=255)

                                                                              tACACTAGAATTGTTATTAGCTTGCGGTTTATCCTTTGCATCATCAGTTGCTGATGTTACTGCTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAg                                                        <  1:371521/140‑1 (MQ=255)

                                                                              tACACTAGAATTGTTATTAGCTTGCGGTTTAGCATTGGCATCTTGAAGGACCTATTTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAg                                                        <  1:536897/140‑1 (MQ=255)

                                                                              ggtgcTAGTATTGTGACTAGCCGGCCGTTTATCATTTGCATCATCAGCGCCTGATGCTACTGTTGTTTCCCCTGCTGCCGCATCACTATTATTTTGGGTTGTCGGAGAATCGGCTGCTTTGCCATTCGCCGGTGTCTCAg                                                        <  2:213693/136‑1 (MQ=255)

                                                                                       aTTGTTATTAGCTTGCGGTTTATCATATGCATCATCAGTTGCTTTTGTTACTGTTGTTTCACCTGTTGCCGAATCACTATTATTTGGTGTTGTTGGGGAAGCGTCTGCGTTGCCATTATCTGTCGTCTTCGGTACGGTAg                                               >  2:329398/1‑140 (MQ=255)

                                                                                           ttattaGCTTGCGGTTTATCATGTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTg                                           >  2:4790/1‑140 (MQ=255)

                                                                                            tattaGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCGTTGCCATTAGCTGTCGTCTCCGATCCGTTAGGTTGt                                          >  2:326318/1‑140 (MQ=255)

                                                                                            tattaGCTGGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTACCTGTCGTCTCAGAAACGTTAGGTTGt                                          >  2:346834/1‑140 (MQ=255)

                                                                                                tgCTTGGGGTTGTTCATTTGGTTCATCAGTTTCTTATGTTACTGTTGTTTCACCTGTTGCCGCATCCCTATTATTTGGTGTTTTCGGAGAAGGGTCTGCTTTGCCATTAGTTGTCGTCTCAGATACGTTAGGTTGTCCAg                                      <  2:263045/139‑1 (MQ=255)

                                                                                                      cGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTAtttt                                >  1:54800/1‑140 (MQ=255)

                                                                                                        gTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTCGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCt                              <  2:375840/140‑1 (MQ=255)

                                                                                                           tATCGTGTGCATCATCAGTTGCTGATGATACTGTTGTTTCACCTATTGCCGTAACCCGCTACAGCGCGGTGGTCGGTGTGGCGGCTGCTTTGCCGTAGGCGGGCGTCTCAGATACGTGAGGCTGTCCAGTATTTTCTgat                           >  2:223883/1‑138 (MQ=255)

                                                                                                                     atcatcAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTACGTTGTCCAGTATTTTCTGGTGTTGCATTAg                 >  2:150726/1‑140 (MQ=255)

                                                                                                                     atcatcAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCGGTCGTCTCAGATACGTTAGGTTGTCCAGTGTTTTCTGGTGTTGCATTAg                 >  2:172672/1‑140 (MQ=255)

                                                                                                                      tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCCCTATTATTTGGTGTTGTCGGAGAAGCGTATGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGc                >  1:235235/1‑140 (MQ=255)

                                                                                                                      tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTATCTGTCGTCTCAGATACGTTAGATTGTCCAGTATTTTCTGGTGTTGCATTAGc                >  2:126095/1‑140 (MQ=255)

                                                                                                                      tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCGGGTGTTGCATTacc                >  2:265874/1‑138 (MQ=255)

                                                                                                                        atcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAt              <  2:54800/140‑1 (MQ=255)

                                                                                                                          caGTTGCTGATGTTACTGTTGTTTCACCTTTTGCCGCATCACTATTATTTGGTTTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAttt            <  1:506664/140‑1 (MQ=255)

                                                                                                                                  gATGTTACTTTTTTTTCACCTGTTGCCGCATCACTTTTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGc    <  1:415005/140‑1 (MQ=255)

                                                                                                                                    tGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTg  <  2:446425/140‑1 (MQ=255)

TGTGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTG  >  USA300TCH1516_ALE/2279569‑2279840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A