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
A17 F172 I0 R1	42	33.2	716278	96.8%	693357	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,289,252	C→A	100%	A80S (GCT→TCT)	USA300HOU_2153 ←	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,289,252	0	C	A	100.0%	85.6 / NA	32	A80S (GCT→TCT)	USA300HOU_2153	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (15/17); total (15/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAG  >  CP000730/2289119‑2289385

gCCTTTGAAACCGATTGAATCAATTTATCTTCAACTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATAc                                                                                                                                 <  1:143042/140‑1 (MQ=255)

 ccTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATAcc                                                                                                                                >  2:256291/1‑140 (MQ=255)

  cTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCCAATTTCTGGTTGGAATATTACTATTAAAGATAATAccc                                                                                                                               <  2:309643/140‑1 (MQ=255)

               tGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAAc                                                                                                                  <  1:303363/140‑1 (MQ=255)

                   tCAATTTCTCTTCATTTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGata                                                                                                              <  1:87526/140‑1 (MQ=255)

                       tgtctcTTCATCTTTACTATACTTATTATAAGTATAGCTTTTTAAAAAGCTACCTCTACCAAGTTTTTCTAACGCACGTATAATTTCTTGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGa                                                                                                          <  1:105938/138‑1 (MQ=255)

                            ctTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGaataat                                                                                                     >  1:150877/1‑140 (MQ=255)

                            ctTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGaataat                                                                                                     >  2:208731/1‑140 (MQ=255)

                                   tttACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTGCCTCTACCACGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATGCCCCCCATTAAATCACGATATCGAATAATATAAATg                                                                                              >  1:147213/1‑140 (MQ=255)

                                      aCTATACGTATGAGAAGTATAGCGGTTTATAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATCTTACTATAACACATTATACACCGCATGGAATAATGATATCGAGTAATTTAGATGTTg                                                                                           >  2:250215/1‑140 (MQ=255)

                                            cGTATTAGAAGGATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCa                                                                                     <  2:102755/140‑1 (MQ=255)

                                                 tAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTc                                                                                >  2:274957/1‑140 (MQ=255)

                                                  aGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCa                                                                               >  2:43899/1‑140 (MQ=255)

                                                     aGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGATCAata                                                                            >  1:68588/1‑140 (MQ=255)

                                                      gTATAGCGTCTTAAACAGCTACCTCTACCCAGCGGTTCTAACGCACGTCTAATTTCTCGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTATATGTTTCAGTCAAGTTCAatat                                                                           <  2:296012/140‑1 (MQ=255)

                                                             gatttAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTAGTTGGAATATTACTATTAAAGATAATACCCCCCATAGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACtt                                                                    >  2:263353/3‑140 (MQ=255)

                                                             gTTTTAAAAAGCTACCTCTTCCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACtt                                                                    <  2:339713/140‑1 (MQ=255)

                                                              ttttAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTa                                                                   <  2:149124/140‑1 (MQ=255)

                                                                    aaaGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCTTACTTATctgct                                                             >  2:237076/1‑140 (MQ=255)

                                                                       gCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATCATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGAc                                                          >  2:64669/1‑140 (MQ=255)

                                                                                aCCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCCTTGAACAACGATATCGAAAACTTTAGATCTTGCAGTCAAATTCAATATCACAAATCTCTCCTGACCCAGAAccc                                                 >  2:349852/1‑138 (MQ=255)

                                                                                     ggcttgcTAAAGAACGTCTAATTTCCGGTTGGAATATCACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAAAAATTTAGATGTTCCAGTCAAGTTCAACATCATACTTATCTGCTGACCAATAACAATTACt                                            <  2:139678/134‑1 (MQ=255)

                                                                                          tCTAACGCACGTATAATTTTTGGTTGAAATATTAATAATAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAatat                                       <  1:322904/140‑1 (MQ=255)

                                                                                             aacgaacgTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGAACAATAACAATTACTAATATccc                                    <  2:236544/140‑1 (MQ=255)

                                                                                                  aCGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTaa                               >  1:108173/1‑140 (MQ=255)

                                                                                                       tAATGTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATATTTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTTACCATTATCAATTACTTATATCCCTTTAAGTTAt                          <  2:115833/140‑1 (MQ=255)

                                                                                                        aaTTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTAAAGTTCAAAAGTATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTAAAATAAtt                         >  1:276445/1‑140 (MQ=255)

                                                                                                         aTTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTg                        <  2:61374/140‑1 (MQ=255)

                                                                                                               ggTTGGCATATCACTATTAAAGATAATACCCCCCATTGAATATCGACATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGc                  <  2:137656/140‑1 (MQ=255)

                                                                                                               ggTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGc                  <  2:108173/140‑1 (MQ=255)

                                                                                                                     tatatTACTATTAACGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGt            <  2:187013/139‑1 (MQ=255)

                                                                                                                               ttAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAg  >  2:184137/1‑140 (MQ=255)

GCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAG  >  CP000730/2289119‑2289385

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