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 I1 R1	59	38.6	831760	90.8%	755238	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,502,887	(A)_5→6	coding (1411/2106 nt)	USA300HOU_2364 →	AraC transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,502,882	1	.	A	100.0%	98.9 / NA	30	S469* (TCA→TAA)	USA300HOU_2364	AraC transcriptional regulator
Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (11/19); total (11/19)

TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT  >  CP000730/2502736‑2503010

tCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTTAAAATTC‑a                                                                                                                                 >  1:84941/1‑148 (MQ=255)

       aaaattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaaaact                                                                                                                          <  2:17612/148‑4 (MQ=255)

         aattaaaaACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑aaaaaactgc                                                                                                                        >  2:188087/1‑143 (MQ=255)

                aaCAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACAt                                                                                                                  <  1:244594/148‑1 (MQ=255)

                   aaaaaTAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCtt                                                                                                               <  1:368288/148‑1 (MQ=255)

                               aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAAc                                                                                                   <  1:273836/148‑1 (MQ=255)

                               aTTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTAATCAAACATAAAACAAGTTTATAATGTCATGCAGCGTCTAAAATTCCATTACTACTTTATTTATAAAAAAAAATAAAAAAACTGCAACACAACTTAACACTAAAAAc                                                                                                   <  2:240870/148‑1 (MQ=255)

                                   aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAac                                                                                               >  1:249376/1‑148 (MQ=255)

                                   aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAac                                                                                               >  2:309489/1‑148 (MQ=255)

                                   aaTATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAac                                                                                               >  1:238454/1‑148 (MQ=255)

                                                aGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAAc                                                                                  >  1:386394/1‑148 (MQ=255)

                                                   cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa                                                                               <  1:49801/148‑1 (MQ=255)

                                                   cGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGa                                                                               <  2:263328/148‑1 (MQ=255)

                                                     aTGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGaca                                                                             <  1:46049/148‑1 (MQ=255)

                                                       ggCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACt                                                                           >  1:248183/1‑148 (MQ=255)

                                                          tttttAGAAACTTATTCAAACGTGAAACAAGTTTATAATGACATTCAGCATCTTAAATTCCATTATTACTTTATTAATAAAAAAAAATCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAt                                                                        <  2:286858/148‑1 (MQ=255)

                                                             ttAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCAtttt                                                                     <  2:301221/148‑1 (MQ=255)

                                                                  aaCTTATTCACCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa                                                                <  1:355651/148‑1 (MQ=255)

                                                                  aaCTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACa                                                                <  1:355653/148‑1 (MQ=255)

                                                                          cAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGa                                                        <  2:248183/148‑1 (MQ=255)

                                                                           aaCCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGaa                                                       <  1:380535/148‑1 (MQ=255)

                                                                                tGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAattta                                                  <  2:347847/148‑1 (MQ=255)

                                                                                 ggAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAatttat                                                 <  1:149173/148‑1 (MQ=255)

                                                                                    aCAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTAtttt                                              >  2:195533/1‑148 (MQ=255)

                                                                                     cAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTa                                             <  2:125307/148‑1 (MQ=255)

                                                                                         tttATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGAtt                                         >  1:51289/1‑148 (MQ=255)

                                                                                                 gTCATGCAGCGTCTTAAATTCCATTAGTACTTTATTGATAAAAAAAAAACAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGtata                                 <  2:45503/148‑1 (MQ=255)

                                                                                                               tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt                   <  2:46386/148‑1 (MQ=255)

                                                                                                               tAAATTCCATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAAtt                   <  2:109694/148‑1 (MQ=255)

                                                                                                                     ccATTATTACTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGtata             >  2:1077/1‑148 (MQ=255)

                                                                                                                         tattaCTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat         >  2:361432/1‑148 (MQ=255)

                                                                                                                         tactaCTTTATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATataat         >  2:98863/4‑148 (MQ=255)

                                                                                                                                ttATTGATATTGAAAATTCAAAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACctgt  >  1:148889/1‑148 (MQ=255)

TCATCTTAAAATTAAAAACAAAAATAAAGAAATTAAATATAGTGTGACAGTCGATGGCTTTTTAGAAACTTATTCAACCGTGGAACAAGTTTATGATGTCATGCAGCGTCTTAAATTCCATTATTACTTTATTGATATTGAAAATTC‑AAAAACTGCAACACATCTTATCACTAAAAACCAACACTATCATCAAACTGACACTCATTTTGAACAGTATAAGAAATTTATTTTAGATTCAGGTATATCATCAACACAATTTGTATATAATAACCTGT  >  CP000730/2502736‑2503010

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

GATK/CNVnator alignment

N/A