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 F57 I0 R1	30	26.7	570066	96.5%	550113	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,021,817	C→T	23.3%	V139I (GTT→ATT)	USA300HOU_1873 ←	acyl‑CoA hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,021,817	0	C	T	23.3%	52.8 / 10.9	30	V139I (GTT→ATT)	USA300HOU_1873	acyl‑CoA hydrolase
Reads supporting (aligned to +/- strand): ref base C (17/6); new base T (2/5); total (19/11)
Fisher's exact test for biased strand distribution p-value = 6.80e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

AACAATCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCACT  >  CP000730/2021681‑2021953

aaCAATCTGTCTTTATTTTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAAcatca                                                                                                                                      <  1:106398/141‑1 (MQ=255)

      cTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCAtcttct                                                                                                                                >  1:260829/1‑141 (MQ=255)

         tCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGa                                                                                                                             >  1:169851/1‑141 (MQ=255)

          cTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGat                                                                                                                            <  1:215042/141‑1 (MQ=255)

                atTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATacac                                                                                                                      <  1:38753/141‑1 (MQ=255)

                 tttttAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTCTGATAAAACCCTTTTTCAACATCATCTTCTGGATATACAcc                                                                                                                     >  1:236277/1‑141 (MQ=255)

                 tttttAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACAcc                                                                                                                     >  1:61573/1‑141 (MQ=255)

                       gTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTAc                                                                                                               >  1:238642/1‑141 (MQ=255)

                        tctcTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACa                                                                                                              <  2:192159/141‑1 (MQ=255)

                            tAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGtt                                                                                                          <  1:260451/141‑1 (MQ=255)

                                 tGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGt                                                                                                     <  1:278268/141‑1 (MQ=255)

                                  gTTGCGCTCGATCTGAATCTTCAATTGGTTGTTTATTTTTAATGCTACGTGCTTTTCTTCGTTCTGCACGTTGTGGTGCTGTTTCATAAAACCATTTTTCAACATCATCTTCTAGGTTTACATCATGTATATCTTTAGGtt                                                                                                    >  2:159822/1‑141 (MQ=255)

                                  gTTACACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGtt                                                                                                    >  2:174419/1‑141 (MQ=255)

                                      cACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGcc                                                                                                >  2:257418/1‑141 (MQ=255)

                                          tGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCTTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTtca                                                                                            <  1:78342/141‑1 (MQ=255)

                                           gAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATTTACACCAGGTACATGTGTTGGTTTGCCTtcac                                                                                           >  1:97076/1‑140 (MQ=255)

                                                aaaTATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTTCATGTTTAGGTTTGCCTTCATCATCt                                                                                      <  2:201184/141‑1 (MQ=255)

                                                    atTCAATTGTTTGTTTACTTTCAATGCGAGGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACg                                                                                  >  1:208655/1‑141 (MQ=255)

                                                              ttgtttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGCATATACACCAGGTACATGTTTAGGTGTGCCTTCTTCATCTAACGCAACAAATGt                                                                        <  1:183871/141‑1 (MQ=255)

                                                               cgtttACATTCAATGAGAGGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCACAAAACCATTTTTCAATATCATCTTATGGATATACACAAGGTACATGTTTAGGTTTGCCTTCAACATCTGACGCAAACAATGtt                                                                       >  2:188419/2‑141 (MQ=255)

                                                                gtttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAGTGTTa                                                                      >  1:44379/1‑141 (MQ=255)

                                                                     cTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTaa                                                                 >  1:131450/1‑141 (MQ=255)

                                                                          aaTGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACCCAACACATGGAAAGTAACTTaa                                                            >  2:22582/1‑141 (MQ=255)

                                                                                 cGTGCTTTTCTTCGTTCACCACGATTTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCt                                                     >  2:131009/1‑141 (MQ=255)

                                                                                                tCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTAAAGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGttt                                      >  2:111987/1‑140 (MQ=255)

                                                                                                              tgCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTc                        <  1:144389/141‑1 (MQ=255)

                                                                                                               gCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCa                       <  2:260829/141‑1 (MQ=255)

                                                                                                                      cATAAAACCATTTTTCAACATCATCTTCTGGAGATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGTTAAATCATGCTTGTTATTAAATACATCGTCAATTCTaa                >  1:114109/1‑141 (MQ=255)

                                                                                                                              cATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTCTTCAATCTATCGTCCATTCTATTTTGCACg        <  2:166411/141‑1 (MQ=255)

                                                                                                                                   ttCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCAc   >  2:33251/1‑141 (MQ=255)

                                                                                                                                    tCAACATCATCTTCTGGATAACCCGTCTGAACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTATTATTAAATACATCGTCAATTCTACTTTGAACGACCACt  >  2:130838/1‑141 (MQ=255)

AACAATCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCACT  >  CP000730/2021681‑2021953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A