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 F56 I0 R1	19	43.9	998620	94.5%	943695	140.9

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%	127.9 / ‑6.5	50	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (21/27); total (21/29)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCT  >  USA300TCH1516_ALE/2279571‑2279839

tttcGTTATTAGCTGTTTGTACTTCTGTTTACCTAGTTACATTGTTATGCATTGTCGGACTGTTTGTTGATGCATCTACTCTAGAATTGTTATTAGCTTGCTGTTTATCATTTGCATCATCAGTTGCTGATGTTACtgttg                                                                                                                                  <  2:253508/138‑1 (MQ=255)

tgCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtgttg                                                                                                                                  <  1:445489/141‑1 (MQ=255)

  ccGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGCTGTTACTgttgtt                                                                                                                                >  2:231957/1‑141 (MQ=255)

        ttaGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCt                                                                                                                          <  1:454200/141‑1 (MQ=255)

                   tACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATc                                                                                                               <  1:33921/141‑1 (MQ=255)

                    aCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGAGTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGAATCATAAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCa                                                                                                              >  1:140834/1‑141 (MQ=255)

                    aCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCACCAGTCACTGATGTTACTGTTGTTTCACCTGTTGCCGCATCa                                                                                                              >  1:338977/1‑141 (MQ=255)

                     cTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCAc                                                                                                             <  1:375144/141‑1 (MQ=255)

                        gtGGTGTACTAGTTACGTCGTTATCGATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACtat                                                                                                          <  1:101064/140‑1 (MQ=255)

                         tGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTGGTTGATGCATCTACACGAGAAGAGTTATTGGCTTGCGGTTTATCACTCGCATCATTATTTGTTGCTGTTACTGTTGTTTCACGTGTTGCCGGCTCACtcgt                                                                                                         >  1:42037/1‑138 (MQ=255)

                             ttACTAGTTTCGTTGTTATTCTTTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTAttt                                                                                                     <  2:240530/141‑1 (MQ=255)

                               aCTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTgg                                                                                                   >  1:208658/1‑141 (MQ=255)

                                         tCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATAAGACTGCAGTTTATCATTTGCCTCATCAGTTGCTGATGTTACTGTCGTTTCCCCTGTTGCCGCATCACTCTTATGTTGTGGTCTCggc                                                                                         >  1:191903/1‑140 (MQ=255)

                                               tCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCTGAGAAGCg                                                                                   >  2:409960/1‑141 (MQ=255)

                                                ccATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTATATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGt                                                                                  >  1:253661/1‑141 (MQ=255)

                                                 cATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTc                                                                                 <  1:228153/141‑1 (MQ=255)

                                                  aatgacGGACTGGTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCt                                                                                <  1:64660/136‑1 (MQ=255)

                                                   ttGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTg                                                                               <  2:259302/141‑1 (MQ=255)

                                                       cGGAGTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGGTGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCAGCGCAGCGTCTGcctc                                                                           >  2:396272/1‑138 (MQ=255)

                                                         gACTGGTTGTTGGTGCATCTACACGAGAACTGGTATTAGCTTGCGGTTTATCATTCGCATCATCAATTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATAACTATAATTTGGTGTTGTCGGAGAAGCGTCTGCtttac                                                                         >  2:299885/1‑139 (MQ=255)

                                                           cTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCa                                                                       <  1:408981/141‑1 (MQ=255)

                                                                tgttgGTGTATTTACTCTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCTTCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc                                                                  <  2:191057/141‑1 (MQ=255)

                                                                tgttgATGCATCTTGACTAGAGTTGTTATTAGCTTGCGGTTTATCGTTTGCATCATCAGGTGCTGATGTTTCTGTTGTTTCGCCTGTTGCCGCATCACTATTATTTGGTATTATAGGGGAGGGGTCTGCTTTGCTATTAGc                                                                  <  2:229402/141‑1 (MQ=255)

                                                                tgttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc                                                                  <  2:101894/141‑1 (MQ=255)

                                                                 gttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCt                                                                 <  2:462179/141‑1 (MQ=255)

                                                                     ttgctgcTACACTAGAATTGTTATTAGTTTGCGGTTTATCATTTGCATCATTAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtcg                                                             <  1:267788/135‑1 (MQ=255)

                                                                     aTGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTgtcg                                                             >  1:354591/1‑141 (MQ=255)

                                                                            tACACTAGAATCGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTTATGTTACTGTTTTTTCTACTTTTTTCTTATAACTATTATTTGGGGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGa                                                      <  1:61695/141‑1 (MQ=255)

                                                                              cacTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATa                                                    >  1:402151/1‑141 (MQ=255)

                                                                              cacTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATa                                                    <  1:301938/141‑1 (MQ=255)

                                                                               acTATAATTGTTATTAGCTTGCGTTTTATCATTGGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCATTATTTTTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATAc                                                   <  2:289457/141‑1 (MQ=255)

                                                                                  tgAATTGTTATTAGCTTGCGGTTTATCATTTTCTTCATTTATTCTTTATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGtt                                                <  2:352219/140‑1 (MQ=255)

                                                                                             taGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACCGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGAAATAAGCTGGCGTCTCAGATACGTTAGGTTGTCCAg                                     >  1:414111/1‑141 (MQ=255)

                                                                                              aGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGt                                    <  1:482488/141‑1 (MQ=255)

                                                                                                 ttGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCAGCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTAtt                                 >  1:479817/1‑141 (MQ=255)

                                                                                                  tGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTAttt                                <  1:4473/141‑1 (MQ=255)

                                                                                                      ttttATTATTAGCATCATCAGCTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTg                            <  2:140834/140‑1 (MQ=255)

                                                                                                       tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTATCTGTCGTCTCAGATATGTTAGGTTGTCCAGAATTTTTTgc                           >  2:100861/1‑140 (MQ=255)

                                                                                                       tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGCATCATCTTCGTGAAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTgg                           >  2:105159/1‑141 (MQ=255)

                                                                                                       tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTCGCCGCATCACTATTATTTGGTGTTGTCGGATACGAGTCTCCTCTGTGGTTGGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTgg                           >  2:105219/1‑141 (MQ=255)

                                                                                                       tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTATTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTACAGTATTTTCTgg                           >  1:473316/1‑141 (MQ=255)

                                                                                                          aTCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTTTGgtgt                        >  1:123362/1‑141 (MQ=255)

                                                                                                              tttGCATCATCAATTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCGGGTGTTGcc                    >  2:23925/1‑140 (MQ=255)

                                                                                                                    tcttcaGGTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTTTTGTCGGAGAAGCGTCTGCTTTGCCATTAGTTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCa              <  2:101220/138‑1 (MQ=255)

                                                                                                                    tcatcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTCGGGTGTCCAGAATTATCTGGTGTCACATTAGcc              >  2:399447/1‑140 (MQ=255)

                                                                                                                      atcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAtt            <  1:320859/141‑1 (MQ=255)

                                                                                                                      atcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAtt            <  1:231957/141‑1 (MQ=255)

                                                                                                                          gTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGaa        <  1:465775/141‑1 (MQ=255)

                                                                                                                          gTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGaa        <  1:456382/141‑1 (MQ=255)

                                                                                                                                gATGTTACTGTTGTTTCCCCTGTTGCCGCATTACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCt  <  2:209994/141‑1 (MQ=255)

TGCCGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCT  >  USA300TCH1516_ALE/2279571‑2279839

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