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
A6 F28 I3 R2	24	47.7	2431847	96.1%	2337004	60.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	minE	1,560,516	C→T	P175S (CCA→TCA)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,560,516	0	C	T	91.4%	101.3 / 2.1	35	P175S (CCA→TCA)	evgS	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand): ref base C (3/0); new base T (18/14); total (21/14)
Fisher's exact test for biased strand distribution p-value = 2.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

AATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATC  >  minE/1560458‑1560579

aaTGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGt                                                       <  1:102244/69‑1 (MQ=255)

aaTGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTaa                                                     <  1:870821/71‑1 (MQ=255)

aaTGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTaa                                                     >  1:752404/1‑71 (MQ=255)

aaTGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTaa                                                     >  1:1419381/1‑71 (MQ=255)

 aTGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAAt                                                    >  1:1054683/1‑71 (MQ=255)

    cGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATtca                                                 >  1:1175455/1‑71 (MQ=255)

    cGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATtca                                                 <  1:2120348/71‑1 (MQ=255)

    cGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATtc                                                  <  1:970023/70‑1 (MQ=255)

         gCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCatcaat                                            <  1:1441202/71‑1 (MQ=255)

          cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCatcaat                                            >  1:302214/1‑70 (MQ=255)

            tACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCAt                                         >  1:117329/1‑71 (MQ=255)

            tACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCAGACGAGGTAATTCATCAATCAt                                         >  1:1543113/1‑71 (MQ=255)

            tACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCAGACGAGGTAATTCATCAATCAt                                         >  1:206455/1‑71 (MQ=255)

               cTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAg                                                              <  1:1436629/47‑1 (MQ=255)

               cTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATtca                                                 >  1:34878/1‑60 (MQ=255)

                tCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATtcatc                                               <  1:1590229/61‑1 (MQ=255)

                tCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATtcatc                                               <  1:752368/61‑1 (MQ=255)

                 cACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAg                                                              >  1:2230470/1‑45 (MQ=255)

                 cACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGAc                                                            >  1:2229255/1‑47 (MQ=255)

                   ccAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCa                                                               <  1:107946/42‑1 (MQ=255)

                    cAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCaa                                   >  1:1009676/1‑69 (MQ=255)

                       aaCCAGTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGc                               >  1:2157842/1‑70 (MQ=255)

                            gTAAATATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAAt                         >  1:1647907/1‑71 (MQ=255)

                               aaTATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTa                       >  1:1914827/1‑70 (MQ=255)

                               aaTATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAt                      >  1:1919834/1‑71 (MQ=255)

                               aaTATTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAt                      <  1:700698/71‑1 (MQ=255)

                                atatTGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAtc                     >  1:1346657/1‑71 (MQ=255)

                                   ttGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATctct                  <  1:2226855/71‑1 (MQ=255)

                                    tGCTCGGGTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCa                                    >  1:1519720/1‑52 (MQ=255)

                                           gTAGCAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAtctc                   <  1:1194319/62‑1 (MQ=255)

                                              gCAAATTACCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaaca                           >  1:752569/1‑51 (MQ=255)

                                               cAAATTACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt         <  1:441391/68‑1 (MQ=255)

                                                   ttACCCCTCAGACGAGGTAATTCATCAATCATTTCCaaaa                                 >  1:202474/1‑40 (MQ=255)

                                                   ttACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTatat   >  1:834827/1‑70 (MQ=255)

                                                   ttACCCCTCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc  <  1:2025857/71‑1 (MQ=255)

                                                       ccctcAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa                             <  1:770853/40‑1 (MQ=255)

AATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATC  >  minE/1560458‑1560579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A