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 F8 I0 R1	311	50.1	4085234	95.9%	3917739	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,832,787	T→C	16.3%	M304V (ATG→GTG)	astC ←	succinylornithine transaminase, PLP‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,832,787	0	T	C	16.3%	113.6 / 16.3	50	M304V (ATG→GTG)	astC	succinylornithine transaminase, PLP‑dependent
Reads supporting (aligned to +/- strand): ref base T (14/27); new base C (5/3); total (19/31)
Fisher's exact test for biased strand distribution p-value = 2.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGGTGATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGCCATAGGT  >  W3110S.gb/1832722‑1832856

gCGGTGATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTg                                                                  >  1:869702/1‑71 (MQ=255)

gCGGTGATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTg                                                                  >  1:1581153/1‑71 (MQ=255)

gCGGTGATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCACCTCTg                                                                  >  1:1197461/1‑71 (MQ=255)

     gATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGgtgtg                                                             >  1:3023543/1‑71 (MQ=255)

     gATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGgtgtg                                                             >  1:1528037/1‑71 (MQ=255)

       ttAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:1490792/71‑1 (MQ=255)

       ttAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:1206268/71‑1 (MQ=255)

       ttAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:2111159/71‑1 (MQ=255)

       ttAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCACCTCTGGTGTGtt                                                           <  1:3066210/71‑1 (MQ=255)

       ttAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCACCTCTGGTGTGtt                                                           <  1:1724414/71‑1 (MQ=255)

            aGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCAcct                                                                     >  1:1510645/1‑56 (MQ=255)

              tATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGc                                                    >  1:518364/1‑71 (MQ=255)

                ttAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCAtctc                                                                    <  1:1338883/53‑1 (MQ=255)

                ttAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGgtg                                                               <  1:2272728/58‑1 (MQ=255)

                ttAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTtg                                                          <  1:3041760/63‑1 (MQ=255)

                ttAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTc                                                  >  1:3599145/1‑71 (MQ=255)

                 tAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTc                                                  >  1:1904650/1‑70 (MQ=255)

                  aaGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTtgatga                                                      >  1:2093978/1‑65 (MQ=255)

                  aaGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTtgatga                                                      >  1:2789269/1‑65 (MQ=255)

                   aGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAg                                               <  1:3016102/71‑1 (MQ=255)

                     aCGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGgt                                                                <  1:3814438/52‑1 (MQ=255)

                     aCGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGgt                                                                <  1:3545114/52‑1 (MQ=255)

                     aCGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGgt                                                                <  1:3060855/52‑1 (MQ=255)

                      cGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCAc                                            <  1:1248201/71‑1 (MQ=255)

                       gCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCAc                                            <  1:1807120/70‑1 (MQ=255)

                          caacaaACCAGTCGTGACGCTGTTTAACGCCATTAAGCACCTCTGGTGTGTTGATGAGCTCCAGCACTTtg                                        >  1:3805146/1‑71 (MQ=255)

                          caacaaACCAGTCGTGACGCTGTTTAACGCCATTAAGCACCTCTGGTGTGTTGATGAGCTCCAGCACTTtg                                        >  1:1623368/1‑71 (MQ=255)

                           aacaaACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:2280389/51‑1 (MQ=255)

                           aacaaACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACttt                                         <  1:282474/69‑1 (MQ=255)

                           aacaaACCAGTCGTGACGCTGTTTAACGCCATTAAGCAGCTCTGgt                                                                <  1:3549635/46‑1 (MQ=255)

                              aaaCCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTtgcctg                                    >  1:4078687/1‑71 (MQ=255)

                               aaCCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTtgcctgc                                   >  1:3245969/1‑71 (MQ=255)

                                 ccAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTtgcctgcc                                  >  1:736192/1‑70 (MQ=255)

                                 ccAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCa                                 >  1:1532482/1‑71 (MQ=255)

                                     tCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:1320751/41‑1 (MQ=255)

                                     tCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:2305079/41‑1 (MQ=255)

                                     tCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGtt                                                           <  1:2980223/41‑1 (MQ=255)

                                       gTGACGCTGTTTAACGCCATTAAGCACCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCAccgcc                            >  1:1373195/1‑70 (MQ=255)

                                          aCGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAg                         <  1:3310427/70‑1 (MQ=255)

                                                tttAACGCCATTAAGCATCTCTGGTGTGTttatga                                                      <  1:2100505/35‑1 (MQ=255)

                                                tttAACGCCATTAAGCATCTCTGGTGTGTttatga                                                      <  1:3976928/35‑1 (MQ=255)

                                                tttAACGCCATTAAGCATCTCTGGTGTGTtgatga                                                      <  1:3191152/35‑1 (MQ=255)

                                                tttAACGCCATTAAGCATCTCTGGTGTGTtgatga                                                      <  1:762381/35‑1 (MQ=255)

                                                tttAACGCCATTAAGCATCTCTGGTGTGTtgatga                                                      <  1:1589323/35‑1 (MQ=255)

                                                 ttAACGCCATTAAGCACCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCa                                 >  1:2198050/1‑55 (MQ=255)

                                                         aTTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGc         <  1:1862389/71‑1 (MQ=255)

                                                         aTTAAGCACCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGc         <  1:1071169/71‑1 (MQ=255)

                                                          ttAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCg                  <  1:3199053/61‑1 (MQ=255)

                                                           tAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGCCa       >  1:189914/1‑71 (MQ=255)

                                                              gCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGCCAt      <  1:212309/69‑1 (MQ=255)

                                                               cATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGCCAt      <  1:2274671/68‑1 (MQ=255)

                                                                aTCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGCCATAggt  <  1:2852734/71‑1 (MQ=255)

                                                                 tctcTGGTGTGTTTATGAGCTCCAGCACTTTGCCTGCCAccgcc                            <  1:736460/44‑1 (MQ=255)

                                                                 tctcTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCAccgcc                            <  1:3329003/44‑1 (MQ=255)

GCGGTGATTAATAGTATTAAGACGCTCAACAAACCAGTCGTGACGCTGTTTAACGCCATTAAGCATCTCTGGTGTGTTGATGAGCTCCAGCACTTTGCCTGCCACCGCCGAGGCCAGCGGATTACCGCCATAGGT  >  W3110S.gb/1832722‑1832856

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