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 F13 I0 R1	91	33.2	766976	92.9%	712520	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,021,817	C→T	76.5%	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	76.5%	55.4 / 15.7	39	V139I (GTT→ATT)	USA300HOU_1873	acyl‑CoA hydrolase
Reads supporting (aligned to +/- strand): ref base C (4/5); new base T (17/12); total (22/17)
Fisher's exact test for biased strand distribution p-value = 7.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

TCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCAC  >  CP000730/2021686‑2021952

tCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAAATGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCGGTATCATAAAACCATTTTTCAATATCAtcttc                                                                                                                                >  1:255985/1‑141 (MQ=255)

 cTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCAtcttct                                                                                                                               >  1:207270/1‑141 (MQ=255)

     cTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGat                                                                                                                           >  1:226626/1‑141 (MQ=255)

       ttATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTAAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATAATCTTCTTGatat                                                                                                                         >  1:208796/1‑141 (MQ=255)

        tataTTTTTAGTCTCTAATATGTTACACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGAtata                                                                                                                        >  1:278719/1‑141 (MQ=255)

              tttAGTCTCTAATATGTTTCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAg                                                                                                                  <  2:45026/141‑1 (MQ=255)

                     tctAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATg                                                                                                           <  1:335481/141‑1 (MQ=255)

                     tctAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTAGTTCAACACGTTGTGGTGCTGTATAATGAAACCGTTTTTCAATATCATCTTCTGGATATACACCGGGTACATg                                                                                                           >  1:244135/1‑141 (MQ=255)

                      tttttatGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCATCTCGTTTTTTTTTTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACTCCACGTACATGt                                                                                                          >  2:278265/5‑141 (MQ=255)

                       tAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACAGCAGGTACATGtt                                                                                                         >  2:87595/1‑141 (MQ=255)

                            tGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATCTACACCCGGTACATGTTTAGGt                                                                                                    >  1:36334/1‑141 (MQ=255)

                            tGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTCTTATTCGTTCAACACGTTGTGGTGCTTTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGt                                                                                                    >  2:348884/1‑141 (MQ=255)

                              ttccACTTGAGCTAAATACTCACTTGTTTGTTTACTTTCAATGCAACATCCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAAACATTTTTCAATACCATCTTCTGGATATACACCAGGTACATGTTTAGGttt                                                                                                  <  2:382940/138‑1 (MQ=255)

                              ttGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGttt                                                                                                  <  2:324045/141‑1 (MQ=255)

                                gCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGtttcc                                                                                                >  2:137105/1‑139 (MQ=255)

                                gCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTATTCTTCGTTCAACGCGTTGTGGTGCTGTATCATAAAACCATTTTTTACGATCATCTTCTGGATATACACCAGGTACATGTTTAGGGTTGc                                                                                                >  2:61633/1‑141 (MQ=255)

                                      gAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGATACATGGTTAGGTTTGCCTtcat                                                                                          >  2:215571/1‑141 (MQ=255)

                                      gAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTtcat                                                                                          <  1:368803/141‑1 (MQ=255)

                                          tAAATATTCAATTGTTTGTTTACTTCCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCatcatc                                                                                      <  2:322435/141‑1 (MQ=255)

                                             attttCCATTGTTTGTTTACTTTAAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTaa                                                                                   <  2:85603/138‑1 (MQ=255)

                                                       gtttgtttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAAt                                                                         <  1:33015/141‑1 (MQ=255)

                                                         ttgtttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGt                                                                       <  1:369940/141‑1 (MQ=255)

                                                          tgtttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGtt                                                                      >  1:304113/1‑141 (MQ=255)

                                                            tttACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAAGGTTaa                                                                    >  2:203181/1‑141 (MQ=255)

                                                            tttACTTTCAATGCGACGTGCTTTTCTTAGTTCTACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATAAACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTaa                                                                    >  1:378467/1‑141 (MQ=255)

                                                                    cAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTa                                                            <  2:14048/141‑1 (MQ=255)

                                                                                  tttCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCa                                              >  1:338520/1‑141 (MQ=255)

                                                                                    tcttcGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATg                                            <  2:235331/141‑1 (MQ=255)

                                                                                       tcGTTCAACTCTGTGTGGTGCTGTAGCATAAAACCATTTTTCATCATTATCTTCTGGATATAATCTAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCtt                                         <  2:123709/141‑1 (MQ=255)

                                                                                       tcGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCtt                                         <  2:56790/141‑1 (MQ=255)

                                                                                        cGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATTCTTTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTg                                        <  1:10955/141‑1 (MQ=255)

                                                                                         gTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGt                                       >  1:213320/1‑141 (MQ=255)

                                                                                          ttCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGtt                                      <  1:38321/141‑1 (MQ=255)

                                                                                                          gCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATATATCGTCa                      >  1:113376/1‑141 (MQ=255)

                                                                                                          gCTGTATCATAAAACCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCa                      >  1:170237/1‑141 (MQ=255)

                                                                                                                       aCCATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTCTTAAATACATCGTCAATTCTAATTTGaa         >  1:265665/1‑141 (MQ=255)

                                                                                                                        ccATTTTTCAATATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAAc        <  2:343678/141‑1 (MQ=255)

                                                                                                                            ttttCACTATCATCTCCGTGATATACACCAGTTACCTGGTTAGGTTTGCCCTCCTCATCTAACGCAACAAATGTTAAGTAACTTAATGCATCTAAATCATGCTTTTCATTAAATACATCGTCCATTCTAATTTGAACGAcc    <  2:192187/141‑1 (MQ=255)

                                                                                                                              ttCAATATCATCGTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATAAAGCTTGATATTAAATACATCGTCAATTCTAATTTGAACGACCAc  >  2:365951/1‑141 (MQ=255)

TCTGTCTTTATATTTTTAGTCTCTAATATGTTGCACTTGAGCTAAATATTCAATTGTTTGTTTACTTTCAATGCGACGTGCTTTTCTTCGTTCAACACGTTGTGGTGCTGTATCATAAAACCATTTTTCAACATCATCTTCTGGATATACACCAGGTACATGTTTAGGTTTGCCTTCATCATCTAACGCAACAAATGTTAAGTAACTTAATGCAGCTAAATCATGCTTGTTATTAAATACATCGTCAATTCTAATTTGAACGACCAC  >  CP000730/2021686‑2021952

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