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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,249,944 C→A 10.4% P89T (CCG→ACG)  yqjG → predicted S‑transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,249,9440CA10.4% 175.5 / 3.9 56P89T (CCG→ACG) yqjGpredicted S‑transferase
Reads supporting (aligned to +/- strand):  ref base C (19/31);  new base A (3/3);  total (22/34)
Fisher's exact test for biased strand distribution p-value = 6.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCGCACGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTAT  >  W3110S.gb/3249878‑3250012
                                                                  |                                                                    
caccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCt                                                                  <  1:2672827/71‑1 (MQ=255)
caccgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACACGCt                                                                  >  1:164707/1‑71 (MQ=255)
 accgcacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGAAGTGAACCCGc                                                                   >  1:2167711/1‑69 (MQ=255)
     cacGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGc                                                             >  1:2122943/1‑71 (MQ=255)
      acGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCt                                                            <  1:4466274/71‑1 (MQ=255)
      acGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCt                                                            <  1:1584318/71‑1 (MQ=255)
      acGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCt                                                            <  1:2273256/71‑1 (MQ=255)
             tCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAAc                                                     >  1:992814/1‑71 (MQ=255)
               aTGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACgg                                                   <  1:2984833/71‑1 (MQ=255)
               aTGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACg                                                    <  1:17899/70‑1 (MQ=255)
                tGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGa                                                         <  1:255837/64‑1 (MQ=255)
                tGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGt                                                  <  1:2369058/71‑1 (MQ=255)
                  cgcAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTg                                                <  1:1499651/71‑1 (MQ=255)
                   gcAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTg                                                >  1:4069565/1‑70 (MQ=255)
                   gcAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCAGTAGTGAACACGCTGATGCTGGaaaa                                                      >  1:3112552/1‑64 (MQ=255)
                       aCTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTTGACCt                                           <  1:298044/71‑1 (MQ=255)
                       aCTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCt                                           <  1:2636564/71‑1 (MQ=255)
                       aCTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCAGCTGATGCTGGAAAACGGTTGGACCt                                           >  1:1644415/1‑71 (MQ=255)
                         tCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTg                                                                 <  1:4135253/47‑1 (MQ=255)
                          cAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAAccc                                                                     <  1:2268208/42‑1 (MQ=255)
                          cAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                         >  1:2235038/1‑70 (MQ=255)
                           aaaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                         <  1:1435037/69‑1 (MQ=255)
                            aaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgat                                      <  1:489170/71‑1 (MQ=255)
                            aaGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAA‑CCGCTGATGCTGGAAAACGGTTGGACCTTtgat                                      >  1:2552889/1‑70 (MQ=255)
                             aGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAAcc                                                                      >  1:1585044/1‑38 (MQ=255)
                             aGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTgg                                                          >  1:3390070/1‑50 (MQ=255)
                             aGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACg                                                    >  1:3615577/1‑56 (MQ=255)
                              ggACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgatga                                    <  1:3620563/71‑1 (MQ=255)
                               gACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgatga                                    <  1:799374/70‑1 (MQ=255)
                                    gAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCt                                                                  <  1:395644/35‑1 (MQ=255)
                                    gAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGttt                              <  1:1785806/71‑1 (MQ=255)
                                    gAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGttt                              <  1:2993006/71‑1 (MQ=255)
                                    gAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGt                                <  1:3615518/69‑1 (MQ=255)
                                      aCCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTc                            >  1:3808356/1‑71 (MQ=255)
                                      aCCGTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGAAAACGGTTGGAcc                                            <  1:1991285/55‑1 (MQ=255)
                                      aCCGTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGAAAACGGTTGGAACTTTGATGACAGTTTTc                            >  1:1459048/1‑71 (MQ=255)
                                       ccGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATg                                                              <  1:2488957/36‑1 (MQ=255)
                                       ccGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGAc                                             <  1:1980586/53‑1 (MQ=255)
                                       ccGTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTcc                           <  1:2097050/71‑1 (MQ=255)
                                       ccGTTTATTTCCGTTTCCGTAGTGAACACGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTcc                           <  1:4024750/71‑1 (MQ=255)
                                        cGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGtt                               <  1:1767822/66‑1 (MQ=255)
                                         gTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGCAAACGGTTGGACCTTTGATGACAGtt                               <  1:4371954/65‑1 (MQ=255)
                                         gTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                         <  1:3810163/55‑1 (MQ=255)
                                         gTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCgg                         <  1:1836807/71‑1 (MQ=255)
                                            tATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCttt                                         >  1:433153/1‑52 (MQ=255)
                                               ttccgtttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCa                    <  1:3108457/70‑1 (MQ=255)
                                                 ccgtttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtga                                       >  1:3516274/1‑49 (MQ=255)
                                                 ccgtttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtga                                       >  1:3521474/1‑49 (MQ=255)
                                                  cgtttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCg                <  1:3260930/71‑1 (MQ=255)
                                                   gtttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAg                                 <  1:1177049/53‑1 (MQ=255)
                                                     ttccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTc                            >  1:2236983/1‑56 (MQ=255)
                                                     ttccgtAGTGAACCAGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCg                >  1:2958987/1‑68 (MQ=255)
                                                      tccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGtt                               >  1:2058307/1‑52 (MQ=255)
                                                      tccgtAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTc                            >  1:4439349/1‑55 (MQ=255)
                                                          tAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtg                                        <  1:3393449/39‑1 (MQ=255)
                                                            gTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTtgat                                      >  1:4546564/1‑39 (MQ=255)
                                                            gTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGttt                              <  1:3820258/47‑1 (MQ=255)
                                                                aCCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGACACACGCTCTAt  >  1:3386408/1‑71 (MQ=255)
                                                                 cccGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGc                     <  1:3601662/51‑1 (MQ=255)
                                                                 cccGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGga              >  1:4054322/1‑58 (MQ=255)
                                                                  |                                                                    
CACCGCACGCTGATCATGCGCAAACTCAAAGGACTGGAACCGTTTATTTCCGTTTCCGTAGTGAACCCGCTGATGCTGGAAAACGGTTGGACCTTTGATGACAGTTTTCCGGGAGCAACCGGAGACACGCTCTAT  >  W3110S.gb/3249878‑3250012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A